[ { "_id": 4, "collapsing_method": null, "collection_time_point_relative": "Week 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A2wk1", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065380", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1316424", "cell_number": "2369736", "ir_sequence_count": 1316424, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "35 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278153.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 35, "ir_min_age": 35, "ir_rearrangement_file_name": "ERR1278153_aa.txz, ERR1278153_ab.txz, ERR1278153_ac.txz", "ir_rearrangement_number": 425, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 415, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1316424", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278153_filtered_1.fastq -r ERR1278153_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278153.fastq", "ir_project_sample_id": 4 }, { "_id": 5, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "43123_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619243", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "43213_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9444", "cell_number": null, "ir_sequence_count": 9409, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "34 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298742.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 34, "ir_min_age": 34, "ir_rearrangement_file_name": "SRR1298742.txz", "ir_rearrangement_number": 402, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 392, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "9409", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 5 }, { "_id": 10, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_6-sc-2013-01-11T14:16:57Z-1548384", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6509", "cell_number": "8455", "ir_sequence_count": 6464, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220435.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220435.txz", "ir_rearrangement_number": 364, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 354, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6464", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 10 }, { "_id": 12, "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "44", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "44", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4464", "cell_number": "422073", "ir_sequence_count": 4381, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "44 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode45a.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 44, "ir_min_age": 44, "ir_rearrangement_file_name": "SRR030820_barcode45a.txz", "ir_rearrangement_number": 245, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 235, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4381", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 12 }, { "_id": 14, "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "68", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "68", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8255", "cell_number": "422073", "ir_sequence_count": 8082, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode70.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "SRR030820_barcode70.txz", "ir_rearrangement_number": 261, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 251, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8082", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 14 }, { "_id": 16, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11-sc-2013-01-11T14:16:14Z-1548344", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6331", "cell_number": "6910", "ir_sequence_count": 6315, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220399.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220399.txz", "ir_rearrangement_number": 328, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 318, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6315", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 16 }, { "_id": 19, "collapsing_method": null, "collection_time_point_relative": "Jan-11", "sequencing_facility": null, "cell_phenotype": "CD19+, IgM-, IgD-, IgA-", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, lss8@columbia.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA188191", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "N152-Heavy Chain2", "lab_name": "Kwong Lab", "pcr_target_locus": "IGH", "lab_address": "National Institute of Allergy and Infectious Disease-Vaccine Research Center", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS1415051", "template_amount": null, "submitted_by": "P.D. Kwong, J. Zhu, G. Ofek", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "N152", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "755429", "cell_number": "843084", "ir_sequence_count": 755429, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "20 years", "template_class": "RNA", "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", "pub_ids": "PMID: 23536288", "disease_diagnosis": "HIV", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "filtered_SRR654171heavy_split1.fasta, filtered_SRR654171heavy_split2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "filtered_SRR654171heavy_split1.txz, filtered_SRR654171heavy_split2.txz", "ir_rearrangement_number": 4, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 4, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "755429", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 19 }, { "_id": 17, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-e", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1006", "cell_number": "556038", "ir_sequence_count": 1001, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode5.txz", "ir_rearrangement_number": 208, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 198, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1001", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 17 }, { "_id": 20, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9653", "cell_number": "251408", "ir_sequence_count": 9585, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode13.txz", "ir_rearrangement_number": 130, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 120, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "9585", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 20 }, { "_id": 21, "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "lab_name": "Department of Pathology, Stanford University", "submitted_by": "Boyd S.D, Marshall E.L ", "prior_therapies": null, "cells_per_reaction": null, "read_length": null, "complete_sequences": "partial", "ir_sra_run_id": "SRS007525", "disease_stage": null, "sample_id": "37", "library_generation_kit_version": null, "disease_state_sample": "Healthy", "sex": null, "collapsing_method": null, "sequencing_facility": null, "grants": null, "inclusion_exclusion_criteria": null, "disease_length": null, "primer_match_cutoffs": null, "cell_storage": null, "ethnicity": null, "intervention": null, "synthetic": 0, "physical_linkage": null, "ancestry_population": null, "collected_by": "afire@stanford.edu", "collection_time_point_relative": "Day 0 and 14 months", "subject_id": "37", "sequencing_run_id": null, "disease_diagnosis": "Healthy", "sample_type": null, "single_cell": 0, "race": null, "template_class": "DNA", "cell_phenotype": null, "total_reads_passing_qc_filter": "3811", "link_type": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "pub_ids": "PMID: 20161664", "cell_quality": null, "quality_thresholds": null, "sequencing_kit": null, "template_amount": null, "cell_isolation": null, "study_description": "Cancer Study", "study_group_description": "Control", "cell_processing_protocol": null, "sequencing_run_date": null, "pcr_target_locus": "IGH", "biomaterial_provider": null, "immunogen": null, "strain_name": null, "medical_history": null, "sequencing_platform": "454 GS FLX", "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "linked_subjects": null, "age_event": null, "cell_number": "433784", "template_quality": null, "cell_subset": "Peripheral blood mononuclear cells", "tissue": "Blood", "tissue_processing": null, "study_id": "SRP001460", "lab_address": "Stanford University", "anatomic_site": null, "organism": "Homo sapiens", "ir_sequence_count": 3781, "library_generation_protocol": null, "age": "37 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode37.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "SRR030822_barcode37.txz", "ir_rearrangement_number": 240, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 230, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3781", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 21 }, { "_id": 27, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8-sc-2013-01-11T14:16:23Z-1548351", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8284", "cell_number": "10503", "ir_sequence_count": 8243, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220406.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220406.txz", "ir_rearrangement_number": 335, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 325, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8243", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 27 }, { "_id": 28, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-a", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "12179", "cell_number": "635307", "ir_sequence_count": 12147, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode1.txz", "ir_rearrangement_number": 199, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 189, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "12147", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 28 }, { "_id": 29, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4267", "cell_number": "171714", "ir_sequence_count": 4247, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode2.txz", "ir_rearrangement_number": 146, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 136, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4247", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 29 }, { "_id": 31, "collapsing_method": null, "collection_time_point_relative": "Jan-11", "sequencing_facility": null, "cell_phenotype": "CD19+, IgM-, IgD-, IgA-", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, lss8@columbia.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA188191", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "N152-Heavy Chain1", "lab_name": "Kwong Lab", "pcr_target_locus": "IGH", "lab_address": "National Institute of Allergy and Infectious Disease-Vaccine Research Center", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS1415051", "template_amount": null, "submitted_by": "P.D. Kwong, J. Zhu, G. Ofek", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "N152", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "585083", "cell_number": "647551", "ir_sequence_count": 585083, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "20 years", "template_class": "RNA", "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", "pub_ids": "PMID: 23536288", "disease_diagnosis": "HIV", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "filtered_SRR3458041heavy_split1.fasta, filtered_SRR3458041heavy_split2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "filtered_SRR3458041heavy_split1.txz, filtered_SRR3458041heavy_split2.txz", "ir_rearrangement_number": 3, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 3, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "585083", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 31 }, { "_id": 34, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 2 FL-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 2 FL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3198", "cell_number": "182564", "ir_sequence_count": 3188, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode7.txz", "ir_rearrangement_number": 155, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 145, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3188", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 34 }, { "_id": 36, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3335", "cell_number": "171714", "ir_sequence_count": 3318, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode23.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode23.txz", "ir_rearrangement_number": 188, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 178, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3318", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 36 }, { "_id": 53, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_7-sc-2013-01-11T14:16:51Z-1548378", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3726", "cell_number": "5513", "ir_sequence_count": 3721, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220430.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220430.txz", "ir_rearrangement_number": 359, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 349, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3721", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 53 }, { "_id": 42, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_5_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_5_7-sc-2013-01-11T14:17:29Z-1548416", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7753", "cell_number": "9080", "ir_sequence_count": 7622, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220464.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "ERR220464.txz", "ir_rearrangement_number": 400, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 390, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7622", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 42 }, { "_id": 49, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4747", "cell_number": "171714", "ir_sequence_count": 4731, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode13.txz", "ir_rearrangement_number": 168, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 158, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4731", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 49 }, { "_id": 47, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "15489", "cell_number": "251408", "ir_sequence_count": 15363, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode16.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode16.txz", "ir_rearrangement_number": 136, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 126, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "15363", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 47 }, { "_id": 48, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "13291", "cell_number": "251408", "ir_sequence_count": 13141, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode2.txz", "ir_rearrangement_number": 108, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 98, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "13141", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 48 }, { "_id": 45, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:1000-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:1000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "11244", "cell_number": "270691", "ir_sequence_count": 11151, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode17.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode17.txz", "ir_rearrangement_number": 137, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 127, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "11151", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 45 }, { "_id": 41, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "healthy donor 2-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "healthy donor 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "12016", "cell_number": "251408", "ir_sequence_count": 11911, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode12.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode12.txz", "ir_rearrangement_number": 128, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 118, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "11911", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 41 }, { "_id": 52, "collapsing_method": null, "collection_time_point_relative": "sampled 4/23/2008", "sequencing_facility": null, "cell_phenotype": " CD3-, CD14-, CD19+, CD20+, IgG+, IgM-, RSC3+", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, jmascola@nih.gov", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA195543", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, igblast 1.8.0", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "IAVI 23", "lab_name": "Vaccine Research Center", "pcr_target_locus": "IGL", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS406326", "template_amount": null, "submitted_by": "T. Zhu, J. Zhou, P.D. Kwong, ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "IAVI 23", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "261576", "cell_number": "324668", "ir_sequence_count": 261576, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies", "pub_ids": "PMID: 23911655", "disease_diagnosis": "HIV", "age": ">18 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgVL2", "ir_fasta_file_name": "filtered_SRR800616lambda_split1.fasta, unfiltered_SRR800616lambda_split1.fasta", "ir_germline_database": "IMGT", "ir_library_source": null, "ir_max_age": 999, "ir_min_age": 18, "ir_rearrangement_file_name": "filtered_SRR800616lambda_split1.txz", "ir_rearrangement_number": 18, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 8, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "IGLC", "ir_curator_count": "261576", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 52 }, { "_id": 51, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4657", "cell_number": "182564", "ir_sequence_count": 4636, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode25.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode25.txz", "ir_rearrangement_number": 191, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 181, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4636", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 51 }, { "_id": 55, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5306", "cell_number": "171714", "ir_sequence_count": 5270, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode16.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode16.txz", "ir_rearrangement_number": 174, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 164, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5270", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 55 }, { "_id": 38, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_5-sc-2013-01-11T14:16:28Z-1548355", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5463", "cell_number": "8573", "ir_sequence_count": 5457, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220410.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220410.txz", "ir_rearrangement_number": 339, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 329, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5457", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 38 }, { "_id": 43, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F1Cpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718537", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 1 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1928616", "cell_number": "4401648", "ir_sequence_count": 1928616, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "13 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875290.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 13, "ir_min_age": 13, "ir_rearrangement_file_name": "ERR875290_aa.txz, ERR875290_ab.txz, ERR875290_ac.txz, ERR875290_ad.txz", "ir_rearrangement_number": 444, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 434, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1928616", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875289_filtered_1.fastq -r ERR875289_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875289.fastq", "ir_project_sample_id": 43 }, { "_id": 58, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_8-sc-2013-01-11T14:16:31Z-1548358", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6175", "cell_number": "8836", "ir_sequence_count": 6170, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220413.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220413.txz", "ir_rearrangement_number": 342, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 332, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6170", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 58 }, { "_id": 59, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "26712_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619211", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "26712_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "118607", "cell_number": null, "ir_sequence_count": 117778, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "54 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1297001.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 54, "ir_min_age": 54, "ir_rearrangement_file_name": "SRR1297001.txz", "ir_rearrangement_number": 417, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 407, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "117778", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 59 }, { "_id": 60, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_4-sc-2013-01-11T14:16:34Z-1548361", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4584", "cell_number": "5227", "ir_sequence_count": 4579, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220415.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220415.txz", "ir_rearrangement_number": 344, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 334, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "4579", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 60 }, { "_id": 69, "collapsing_method": null, "collection_time_point_relative": null, "sequencing_facility": null, "cell_phenotype": "IgG+, CD19+, CD20+", "ethnicity": "Hispanic", "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, jmascola@nih.gov", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA195543", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, igblast 1.8.0", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "RU 3", "lab_name": "Vaccine Research Center", "pcr_target_locus": "IGK", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS406331", "template_amount": null, "submitted_by": "T. Zhu, J. Zhou, P.D. Kwong, ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "RU 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1277929", "cell_number": "1400000", "ir_sequence_count": 1277929, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "11 years", "template_class": "RNA", "study_title": "Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies", "pub_ids": "PMID: 23911655", "disease_diagnosis": "HIV", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgVK1, IgVK3", "ir_fasta_file_name": "filtered_SRR800642heavyandlight_split1.fasta, filtered_SRR800642heavyandlight_split2.fasta, filtered_SRR800642heavyandlight_split3.fasta, unfiltered_SRR800642heavyandlight_split1.fasta, unfiltered_SRR800642heavyandlight_split2.fasta, unfiltered_SRR800642heavyandlight_split3.fasta", "ir_germline_database": "IMGT", "ir_library_source": null, "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "filtered_SRR800642heavyandlight_split1.txz, filtered_SRR800642heavyandlight_split2.txz, filtered_SRR800642heavyandlight_split3.txz", "ir_rearrangement_number": 17, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 7, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "IGKC", "ir_curator_count": "1277929", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 69 }, { "_id": 63, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "29612_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619238", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "29612_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5637", "cell_number": null, "ir_sequence_count": 5625, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "22 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298733.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 22, "ir_min_age": 22, "ir_rearrangement_file_name": "SRR1298733.txz", "ir_rearrangement_number": 407, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 397, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "5625", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 63 }, { "_id": 72, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "30512_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619227", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "30512_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "176463", "cell_number": null, "ir_sequence_count": 175140, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "34 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298735.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 34, "ir_min_age": 34, "ir_rearrangement_file_name": "SRR1298735.txz", "ir_rearrangement_number": 414, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 404, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "175140", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 72 }, { "_id": 77, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A1pre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065376", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1821655", "cell_number": "3207806", "ir_sequence_count": 1821655, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "42 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278149.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 42, "ir_min_age": 42, "ir_rearrangement_file_name": "ERR1278149_aa.txz, ERR1278149_ab.txz, ERR1278149_ac.txz, ERR1278149_ad.txz", "ir_rearrangement_number": 429, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 419, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1821655", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875304_filtered_1.fastq -r ERR875304_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875304.fastq", "ir_project_sample_id": 77 }, { "_id": 85, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "34012_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619241", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "34012_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "20873", "cell_number": null, "ir_sequence_count": 20656, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "43 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298738.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 43, "ir_min_age": 43, "ir_rearrangement_file_name": "SRR1298738.txz", "ir_rearrangement_number": 404, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 394, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "20656", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 85 }, { "_id": 81, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-3a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 14 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4705", "cell_number": "182564", "ir_sequence_count": 4682, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode22.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode22.txz", "ir_rearrangement_number": 185, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 175, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4682", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 81 }, { "_id": 82, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "12909", "cell_number": "270691", "ir_sequence_count": 12753, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode3.txz", "ir_rearrangement_number": 109, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 99, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "12753", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 82 }, { "_id": 87, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-c", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3069", "cell_number": "556038", "ir_sequence_count": 3057, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode3.txz", "ir_rearrangement_number": 204, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 194, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3057", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 87 }, { "_id": 86, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Normal control-a1,3", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Normal control", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "13020", "cell_number": "635307", "ir_sequence_count": 12947, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode13.txz", "ir_rearrangement_number": 223, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 213, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "12947", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 86 }, { "_id": 90, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "38", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "38", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2877", "cell_number": "433784", "ir_sequence_count": 2854, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "38 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode42.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 38, "ir_min_age": 38, "ir_rearrangement_file_name": "SRR030822_barcode42.txz", "ir_rearrangement_number": 242, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 232, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2854", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 90 }, { "_id": 94, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8371", "cell_number": "182564", "ir_sequence_count": 8338, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode15.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode15.txz", "ir_rearrangement_number": 171, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 161, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8338", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 94 }, { "_id": 95, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_7-sc-2013-01-11T14:16:58Z-1548385", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7411", "cell_number": "9692", "ir_sequence_count": 7395, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220436.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220436.txz", "ir_rearrangement_number": 365, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 355, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7395", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 95 }, { "_id": 93, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "31012_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619240", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "31012_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "13811", "cell_number": null, "ir_sequence_count": 13686, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "37 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298736.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "SRR1298736.txz", "ir_rearrangement_number": 405, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 395, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "13686", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 93 }, { "_id": 96, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 3 FL and SLL-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 3 FL and SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "15431", "cell_number": "270691", "ir_sequence_count": 15359, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Small Lymphocytic Leukemia, Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode8.txz", "ir_rearrangement_number": 119, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 109, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "15359", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 96 }, { "_id": 97, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "54", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "54", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5911", "cell_number": "433784", "ir_sequence_count": 5842, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "54 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode55.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 54, "ir_min_age": 54, "ir_rearrangement_file_name": "SRR030822_barcode55.txz", "ir_rearrangement_number": 254, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 244, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5842", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 97 }, { "_id": 98, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "10347", "cell_number": "270691", "ir_sequence_count": 10275, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode13.txz", "ir_rearrangement_number": 129, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 119, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "10275", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 98 }, { "_id": 99, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 4 CLL/SLL-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 4 CLL/SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5171", "cell_number": "182564", "ir_sequence_count": 5143, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode9.txz", "ir_rearrangement_number": 159, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 149, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5143", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 99 }, { "_id": 100, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 3 FL and SLL-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 3 FL and SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4951", "cell_number": "171714", "ir_sequence_count": 4932, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Small Lymphocytic Leukemia, Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode8.txz", "ir_rearrangement_number": 158, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 148, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4932", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 100 }, { "_id": 101, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8577", "cell_number": "270691", "ir_sequence_count": 8494, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode15.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode15.txz", "ir_rearrangement_number": 133, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 123, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8494", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 101 }, { "_id": 102, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_3-sc-2013-01-11T14:16:54Z-1548381", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9146", "cell_number": "9931", "ir_sequence_count": 9087, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220432.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220432.txz", "ir_rearrangement_number": 361, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 351, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9087", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 102 }, { "_id": 103, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_6-sc-2013-01-11T14:16:36Z-1548363", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5042", "cell_number": "5624", "ir_sequence_count": 5035, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220417.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220417.txz", "ir_rearrangement_number": 346, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 336, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5035", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 103 }, { "_id": 104, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3269", "cell_number": "171714", "ir_sequence_count": 3256, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode21.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode21.txz", "ir_rearrangement_number": 184, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 174, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3256", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 104 }, { "_id": 105, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Liver tissue", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD liver DLBCL-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD liver DLBCL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4665", "cell_number": "270691", "ir_sequence_count": 4481, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode11.txz", "ir_rearrangement_number": 125, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 115, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4481", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 105 }, { "_id": 110, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Sibling, Mother", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Child A1", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033674", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Child A1", "intervention": null, "linked_subjects": "Child A2, Mother A", "total_reads_passing_qc_filter": "4687578", "cell_number": "4687578", "ir_sequence_count": 3132256, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "11 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "filtered_du_SRR1033674.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 11, "ir_min_age": 11, "ir_rearrangement_file_name": "SRR1033674_mixcr_annotation.txt", "ir_rearrangement_number": 274, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 264, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "3132256", "ir_ancillary_rearrangement_file_name": "SRR1033674_mixcr.vdjca, SRR1033674_mixcr_annotation.txt, SRR1033674_mixcr.clns, SRR1033674_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 110 }, { "_id": 112, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Sibling, Mother", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Child B2", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033677", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Child B2", "intervention": null, "linked_subjects": "Child B1, Mother B", "total_reads_passing_qc_filter": "4615093", "cell_number": "4615093", "ir_sequence_count": 3582672, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "10 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "filtered_du_SRR1033677.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 10, "ir_min_age": 10, "ir_rearrangement_file_name": "SRR1033677_mixcr_annotation.txt", "ir_rearrangement_number": 271, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 261, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "3582672", "ir_ancillary_rearrangement_file_name": "SRR1033677_mixcr.vdjca, SRR1033677_mixcr_annotation.txt, SRR1033677_mixcr.clns, SRR1033677_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 112 }, { "_id": 111, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F3NCpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718546", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 3 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1633051", "cell_number": "2634244", "ir_sequence_count": 1633051, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "4 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875299.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 4, "ir_min_age": 4, "ir_rearrangement_file_name": "ERR875299_aa.txz, ERR875299_ab.txz, ERR875299_ac.txz, ERR875299_ad.txz", "ir_rearrangement_number": 435, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 425, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1633051", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875298_filtered_1.fastq -r ERR875298_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875298.fastq", "ir_project_sample_id": 111 }, { "_id": 113, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "45b", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "45", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5098", "cell_number": "433784", "ir_sequence_count": 5047, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "45 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode50.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 45, "ir_min_age": 45, "ir_rearrangement_file_name": "SRR030822_barcode50.txz", "ir_rearrangement_number": 250, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 240, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5047", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 113 }, { "_id": 114, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F2Cpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": " ERS718542", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 2 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3261822", "cell_number": "5274181", "ir_sequence_count": 3261822, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "12 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875295.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 12, "ir_min_age": 12, "ir_rearrangement_file_name": "ERR875295_aa.txz, ERR875295_ab.txz, ERR875295_ac.txz, ERR875295_ad.txz, ERR875295_ae.txz, ERR875295_af.txz, ERR875295_ag.txz", "ir_rearrangement_number": 439, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 429, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "3261822", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875294_filtered_1.fastq -r ERR875294_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875294.fastq", "ir_project_sample_id": 114 }, { "_id": 116, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Bone marrow", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD marrow infiltrate-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD marrow infiltrate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7021", "cell_number": "251408", "ir_sequence_count": 6935, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode10.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode10.txz", "ir_rearrangement_number": 124, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 114, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6935", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 116 }, { "_id": 115, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-c ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3838", "cell_number": "635307", "ir_sequence_count": 3789, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode9.txz", "ir_rearrangement_number": 215, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 205, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3789", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 115 }, { "_id": 118, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10000-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5636", "cell_number": "182564", "ir_sequence_count": 5612, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode18.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode18.txz", "ir_rearrangement_number": 177, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 167, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5612", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 118 }, { "_id": 119, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F2NCpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718541", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 2 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2257018", "cell_number": "3735856", "ir_sequence_count": 2257018, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "14 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875294.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 14, "ir_min_age": 14, "ir_rearrangement_file_name": "ERR875294_aa.txz, ERR875294_ab.txz, ERR875294_ac.txz, ERR875294_ad.txz, ERR875294_ae.txz", "ir_rearrangement_number": 440, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 430, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2257018", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875293_filtered_1.fastq -r ERR875293_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875293.fastq", "ir_project_sample_id": 119 }, { "_id": 121, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-d", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2006", "cell_number": "635307", "ir_sequence_count": 2000, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode4.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode4.txz", "ir_rearrangement_number": 205, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 195, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2000", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 121 }, { "_id": 123, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "43213_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619231", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "43213_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "162675", "cell_number": null, "ir_sequence_count": 162675, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "34 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298743.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 34, "ir_min_age": 34, "ir_rearrangement_file_name": "SRR1298743.txz", "ir_rearrangement_number": 410, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 400, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "162675", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 123 }, { "_id": 124, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-b", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1893", "cell_number": "635307", "ir_sequence_count": 1885, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode2.txz", "ir_rearrangement_number": 201, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 191, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1885", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 124 }, { "_id": 125, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "44", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "44", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4562", "cell_number": "433784", "ir_sequence_count": 4529, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "44 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode45a.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 44, "ir_min_age": 44, "ir_rearrangement_file_name": "SRR030822_barcode45a.txz", "ir_rearrangement_number": 246, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 236, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4529", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 125 }, { "_id": 126, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_5_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_5_3-sc-2013-01-11T14:17:25Z-1548412", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8225", "cell_number": "9380", "ir_sequence_count": 8136, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220460.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "ERR220460.txz", "ir_rearrangement_number": 396, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 386, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8136", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 126 }, { "_id": 128, "collapsing_method": null, "collection_time_point_relative": "sampled 9/4/2009", "sequencing_facility": null, "cell_phenotype": " CD3-, CD14-, CD19+, CD20+, IgG+, IgM-, RSC3+", "ethnicity": "African", "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, jmascola@nih.gov", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA195543", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, igblast 1.8.0", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and could not run igblast due to pooled light and heavy chains and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "IAVI 57", "lab_name": "Vaccine Research Center", "pcr_target_locus": "IGK", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS406327", "template_amount": null, "submitted_by": "T. Zhu, J. Zhou, P.D. Kwong, ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "IAVI 57", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "501931", "cell_number": "608358", "ir_sequence_count": 501931, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies", "pub_ids": "PMID: 23911655", "disease_diagnosis": "HIV", "age": ">18 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgVK1", "ir_fasta_file_name": "filtered_SRR800639heavyandlight_split1.fasta, filtered_SRR800639heavyandlight_split2.fasta, unfiltered_SRR800639heavyandlight_split1.fasta, unfiltered_SRR800639heavyandlight_split2.fasta", "ir_germline_database": "IMGT", "ir_library_source": null, "ir_max_age": 999, "ir_min_age": 18, "ir_rearrangement_file_name": "filtered_SRR800639heavyandkappa_split1.txz, filtered_SRR800639heavyandkappa_split2.txz", "ir_rearrangement_number": 19, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 9, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "IGKC", "ir_curator_count": "501931", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 128 }, { "_id": 130, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-a", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "10664", "cell_number": "556038", "ir_sequence_count": 10640, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode1.txz", "ir_rearrangement_number": 200, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 190, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "10640", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 130 }, { "_id": 132, "collapsing_method": null, "collection_time_point_relative": "time 3 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-2-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time 3 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7617", "cell_number": "171714", "ir_sequence_count": 7587, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode6.txz", "ir_rearrangement_number": 154, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 144, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7587", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 132 }, { "_id": 134, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_11_barcode3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_11_barcode3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "72007", "cell_number": "116740", "ir_sequence_count": 70976, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode3.txz", "ir_rearrangement_number": 375, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 365, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "70976", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 134 }, { "_id": 138, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "55", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "55", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6331", "cell_number": "433784", "ir_sequence_count": 6253, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "55 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode60.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 55, "ir_min_age": 55, "ir_rearrangement_file_name": "SRR030822_barcode60.txz", "ir_rearrangement_number": 256, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 246, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6253", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 138 }, { "_id": 139, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_8-sc-2013-01-11T14:16:59Z-1548386", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4723", "cell_number": "7171", "ir_sequence_count": 4686, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220437.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220437.txz", "ir_rearrangement_number": 366, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 356, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "4686", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 139 }, { "_id": 140, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "25", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "25", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4530", "cell_number": "433784", "ir_sequence_count": 4479, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "25 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode25.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 25, "ir_min_age": 25, "ir_rearrangement_file_name": "SRR030822_barcode25.txz", "ir_rearrangement_number": 232, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 222, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4479", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 140 }, { "_id": 141, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-a ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5089", "cell_number": "556038", "ir_sequence_count": 5035, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode7.txz", "ir_rearrangement_number": 212, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 202, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5035", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 141 }, { "_id": 144, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3c2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4290", "cell_number": "182564", "ir_sequence_count": 4277, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode28.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode28.txz", "ir_rearrangement_number": 197, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 187, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4277", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 144 }, { "_id": 146, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_6-sc-2013-01-11T14:17:15Z-1548401", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "19653", "cell_number": "32428", "ir_sequence_count": 19408, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "55 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220450.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 55, "ir_min_age": 55, "ir_rearrangement_file_name": "ERR220450.txz", "ir_rearrangement_number": 386, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 376, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "19408", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 146 }, { "_id": 147, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A3pre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065382", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1091249", "cell_number": "2830403", "ir_sequence_count": 1091249, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "47 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278155.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 47, "ir_min_age": 47, "ir_rearrangement_file_name": "ERR1278155_aa.txz, ERR1278155_ab.txz, ERR1278155_ac.txz", "ir_rearrangement_number": 423, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 413, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1091249", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278155_filtered_1.fastq -r ERR1278155_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278155.fastq", "ir_project_sample_id": 147 }, { "_id": 151, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "26712_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619237", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "26712_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4854", "cell_number": null, "ir_sequence_count": 4846, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "54 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298732.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 54, "ir_min_age": 54, "ir_rearrangement_file_name": "SRR1298732.txz", "ir_rearrangement_number": 408, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 398, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "4846", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 151 }, { "_id": 153, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": " 29612_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619226", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "29612_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "149015", "cell_number": null, "ir_sequence_count": 148142, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "22 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298383.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 22, "ir_min_age": 22, "ir_rearrangement_file_name": "SRR1298383.txz", "ir_rearrangement_number": 415, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 405, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "148142", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 153 }, { "_id": 154, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F4Cpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718550", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 4 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1617248", "cell_number": "2706342", "ir_sequence_count": 1617248, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "3 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875303.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 3, "ir_min_age": 3, "ir_rearrangement_file_name": "ERR875303_aa.txz, ERR875303_ab.txz, ERR875303_ac.txz, ERR875303_ad.txz", "ir_rearrangement_number": 431, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 421, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1617248", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875302_filtered_1.fastq -r ERR875302_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875302.fastq", "ir_project_sample_id": 154 }, { "_id": 158, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5191", "cell_number": "182564", "ir_sequence_count": 5179, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode13.txz", "ir_rearrangement_number": 167, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 157, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5179", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 158 }, { "_id": 160, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_11_barcode11", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_11_barcode11", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "25311", "cell_number": "55035", "ir_sequence_count": 8314, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode11.txz", "ir_rearrangement_number": 379, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 369, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8314", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 160 }, { "_id": 164, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6-sc-2013-01-11T14:16:20Z-1548349", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9782", "cell_number": "11580", "ir_sequence_count": 9744, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220404.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220404.txz", "ir_rearrangement_number": 333, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 323, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9744", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 164 }, { "_id": 162, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "19", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "19", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "12377", "cell_number": "422073", "ir_sequence_count": 12119, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "19 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 19, "ir_min_age": 19, "ir_rearrangement_file_name": "SRR030820_barcode19.txz", "ir_rearrangement_number": 225, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 215, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "12119", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 162 }, { "_id": 163, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "14513", "cell_number": "270691", "ir_sequence_count": 14351, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode2.txz", "ir_rearrangement_number": 107, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 97, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "14351", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 163 }, { "_id": 165, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_7-sc-2013-01-11T14:16:44Z-1548371", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9899", "cell_number": "12001", "ir_sequence_count": 9864, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220424.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220424.txz", "ir_rearrangement_number": 353, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 343, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9864", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 165 }, { "_id": 166, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Normal control-a1,3", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Normal control", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "11215", "cell_number": "556038", "ir_sequence_count": 11137, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode13.txz", "ir_rearrangement_number": 224, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 214, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "11137", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 166 }, { "_id": 168, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Bone marrow", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD marrow infiltrate-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD marrow infiltrate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3394", "cell_number": "171714", "ir_sequence_count": 3380, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode10.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode10.txz", "ir_rearrangement_number": 162, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 152, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3380", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 168 }, { "_id": 172, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-b", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1659", "cell_number": "556038", "ir_sequence_count": 1648, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode2.txz", "ir_rearrangement_number": 202, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 192, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1648", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 172 }, { "_id": 171, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4_4-sc-2013-01-11T14:17:19Z-1548406", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5866", "cell_number": "7650", "ir_sequence_count": 5771, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220455.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220455.txz", "ir_rearrangement_number": 391, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 381, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5771", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 171 }, { "_id": 176, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_1", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10-sc-2013-01-11T14:16:13Z-1548343", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8881", "cell_number": "11146", "ir_sequence_count": 8872, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220398.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220398.txz", "ir_rearrangement_number": 327, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 317, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8872", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 176 }, { "_id": 175, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_3-sc-2013-01-11T14:17:01Z-1548388", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7292", "cell_number": "7863", "ir_sequence_count": 7275, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220438.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220438.txz", "ir_rearrangement_number": 367, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 357, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7275", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 175 }, { "_id": 178, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_5-sc-2013-01-11T14:16:19Z-1548348", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "26287", "cell_number": "52242", "ir_sequence_count": 25522, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "59 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220403.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 59, "ir_min_age": 59, "ir_rearrangement_file_name": "ERR220403.txz", "ir_rearrangement_number": 332, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 322, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "25522", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 178 }, { "_id": 179, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Sibling, Mother", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Child A2", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033675", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Child A2", "intervention": null, "linked_subjects": "Child A1, Mother A", "total_reads_passing_qc_filter": "4202419", "cell_number": "4202419", "ir_sequence_count": 3030212, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "9 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "filtered_du_SRR1033675.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 9, "ir_min_age": 9, "ir_rearrangement_file_name": "SRR1033675_mixcr_annotation.txt", "ir_rearrangement_number": 273, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 263, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "3030212", "ir_ancillary_rearrangement_file_name": "SRR1033675_mixcr.vdjca, SRR1033675_mixcr_annotation.txt, SRR1033675_mixcr.clns, SRR1033675_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 179 }, { "_id": 180, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 4 CLL/SLL-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 4 CLL/SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5041", "cell_number": "171714", "ir_sequence_count": 5017, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode9.txz", "ir_rearrangement_number": 160, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 150, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5017", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 180 }, { "_id": 181, "collapsing_method": null, "collection_time_point_relative": "Week 2 ", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A4wk2", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065387", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 4", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1855317", "cell_number": "2033064", "ir_sequence_count": 1855317, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "37 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278160.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "ERR1278160_aa.txz, ERR1278160_ab.txz, ERR1278160_ac.txz, ERR1278160_ad.txz", "ir_rearrangement_number": 418, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 408, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1855317", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278160_filtered_1.fastq -r ERR1278160_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278160.fastq", "ir_project_sample_id": 181 }, { "_id": 182, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4424", "cell_number": "171714", "ir_sequence_count": 4398, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode20.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode20.txz", "ir_rearrangement_number": 182, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 172, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4398", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 182 }, { "_id": 185, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F2Cpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718543", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 2 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2782921", "cell_number": "4373440", "ir_sequence_count": 2782921, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "12 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875296.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 12, "ir_min_age": 12, "ir_rearrangement_file_name": "ERR875296_aa.txz, ERR875296_ab.txz, ERR875296_ac.txz, ERR875296_ad.txz, ERR875296_ae.txz, ERR875296_af.txz", "ir_rearrangement_number": 438, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 428, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2782921", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875295_filtered_1.fastq -r ERR875295_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875295.fastq", "ir_project_sample_id": 185 }, { "_id": 187, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "75", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "75", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6392", "cell_number": "422073", "ir_sequence_count": 6263, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "75 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode78.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 75, "ir_min_age": 75, "ir_rearrangement_file_name": "SRR030820_barcode78.txz", "ir_rearrangement_number": 265, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 255, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6263", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 187 }, { "_id": 2, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "32", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "32", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4219", "cell_number": "433784", "ir_sequence_count": 4182, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "32 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode32.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 32, "ir_min_age": 32, "ir_rearrangement_file_name": "SRR030822_barcode32.txz", "ir_rearrangement_number": 236, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 226, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4182", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 2 }, { "_id": 188, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3355", "cell_number": "171714", "ir_sequence_count": 3334, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode4.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode4.txz", "ir_rearrangement_number": 150, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 140, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3334", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 188 }, { "_id": 190, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 3-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5129", "cell_number": "182564", "ir_sequence_count": 5099, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode14.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode14.txz", "ir_rearrangement_number": 169, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 159, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5099", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 190 }, { "_id": 191, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "20", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "20", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8749", "cell_number": "433784", "ir_sequence_count": 8654, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "20 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode20.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 20, "ir_min_age": 20, "ir_rearrangement_file_name": "SRR030822_barcode20.txz", "ir_rearrangement_number": 228, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 218, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8654", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 191 }, { "_id": 194, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_10_barcode1", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_10_barcode1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "53246", "cell_number": "79153", "ir_sequence_count": 52304, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode1.txz", "ir_rearrangement_number": 374, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 364, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "52304", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 194 }, { "_id": 193, "collapsing_method": null, "collection_time_point_relative": "time 3 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-2a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time 3 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8040", "cell_number": "182564", "ir_sequence_count": 8006, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode6.txz", "ir_rearrangement_number": 153, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 143, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8006", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 193 }, { "_id": 198, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "20", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "20", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8604", "cell_number": "422073", "ir_sequence_count": 8458, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "20 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode20.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 20, "ir_min_age": 20, "ir_rearrangement_file_name": "SRR030820_barcode20.txz", "ir_rearrangement_number": 227, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 217, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8458", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 198 }, { "_id": 195, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:1000-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:1000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "10407", "cell_number": "251408", "ir_sequence_count": 10303, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode17.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode17.txz", "ir_rearrangement_number": 138, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 128, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "10303", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 195 }, { "_id": 199, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "38", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "38", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2843", "cell_number": "422073", "ir_sequence_count": 2794, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "38 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode42.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 38, "ir_min_age": 38, "ir_rearrangement_file_name": "SRR030820_barcode42.txz", "ir_rearrangement_number": 241, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 231, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2794", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 199 }, { "_id": 203, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "75", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "75", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6541", "cell_number": "433784", "ir_sequence_count": 6455, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "75 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode78.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 75, "ir_min_age": 75, "ir_rearrangement_file_name": "SRR030822_barcode78.txz", "ir_rearrangement_number": 266, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 256, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6455", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 203 }, { "_id": 204, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3388", "cell_number": "182564", "ir_sequence_count": 3372, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode27.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode27.txz", "ir_rearrangement_number": 195, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 185, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3372", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 204 }, { "_id": 207, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10000-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "16437", "cell_number": "251408", "ir_sequence_count": 16223, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode18.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode18.txz", "ir_rearrangement_number": 140, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 130, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "16223", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 207 }, { "_id": 210, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "34012_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619229", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "34012_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "97691", "cell_number": null, "ir_sequence_count": 97286, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "43 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298739.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 43, "ir_min_age": 43, "ir_rearrangement_file_name": "SRR1298739.txz", "ir_rearrangement_number": 412, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 402, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "97286", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 210 }, { "_id": 211, "collapsing_method": null, "collection_time_point_relative": "Week 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A1wk1", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065377", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1951899", "cell_number": "3303418", "ir_sequence_count": 1951899, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "42 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278150.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 42, "ir_min_age": 42, "ir_rearrangement_file_name": "ERR1278150_aa.txz, ERR1278150_ab.txz, ERR1278150_ac.txz, ERR1278150_ad.txz", "ir_rearrangement_number": 428, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 418, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1951899", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278150_filtered_1.fastq -r ERR1278150_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278150.fastq", "ir_project_sample_id": 211 }, { "_id": 213, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Liver tissue", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD liver DLBCL-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD liver DLBCL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4506", "cell_number": "251408", "ir_sequence_count": 4302, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode11.txz", "ir_rearrangement_number": 126, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 116, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4302", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 213 }, { "_id": 215, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-f", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3023", "cell_number": "635307", "ir_sequence_count": 3007, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode6.txz", "ir_rearrangement_number": 209, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 199, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3007", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 215 }, { "_id": 216, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_4-sc-2013-01-11T14:16:41Z-1548368", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7902", "cell_number": "10516", "ir_sequence_count": 7892, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220421.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220421.txz", "ir_rearrangement_number": 350, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 340, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7892", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 216 }, { "_id": 218, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 3-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "16655", "cell_number": "251408", "ir_sequence_count": 16525, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode14.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode14.txz", "ir_rearrangement_number": 132, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 122, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "16525", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 218 }, { "_id": 220, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Healthy_1", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_1-sc-2013-01-11T14:17:09Z-1548395", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "30218", "cell_number": "49943", "ir_sequence_count": 29808, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "74 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220444.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 74, "ir_min_age": 74, "ir_rearrangement_file_name": "ERR220444.txz", "ir_rearrangement_number": 373, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 363, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "29808", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 220 }, { "_id": 222, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_8-sc-2013-01-11T14:16:37Z-1548365", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3599", "cell_number": "4427", "ir_sequence_count": 3588, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220419.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220419.txz", "ir_rearrangement_number": 348, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 338, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3588", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 222 }, { "_id": 221, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "60", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "60", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5553", "cell_number": "433784", "ir_sequence_count": 5493, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "60 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode61.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 60, "ir_min_age": 60, "ir_rearrangement_file_name": "SRR030822_barcode61.txz", "ir_rearrangement_number": 258, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 248, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5493", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 221 }, { "_id": 224, "collapsing_method": null, "collection_time_point_relative": "Jan-11", "sequencing_facility": null, "cell_phenotype": "CD19+, IgM-, IgD-, IgA-", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, lss8@columbia.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA188191", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "N152-Light Chain", "lab_name": "Kwong Lab", "pcr_target_locus": "IGL", "lab_address": "National Institute of Allergy and Infectious Disease-Vaccine Research Center", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS1415051", "template_amount": null, "submitted_by": "P.D. Kwong, J. Zhu, G. Ofek", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "N152", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1160314", "cell_number": "1200000", "ir_sequence_count": 1160314, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "20 years", "template_class": "RNA", "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", "pub_ids": "PMID: 23536288", "disease_diagnosis": "HIV", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IGLV", "ir_fasta_file_name": "filtered_SRR654172light_split1.fasta, filtered_SRR654172light_split2.fasta, filtered_SRR654172light_split3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "filtered_SRR654172light_split1.txz, filtered_SRR654172light_split2.txz, filtered_SRR654172light_split3.txz", "ir_rearrangement_number": 5, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 5, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGLC", "ir_curator_count": "1160314", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 224 }, { "_id": 225, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "61", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "61", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9586", "cell_number": "422073", "ir_sequence_count": 9382, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "61 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode68.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 61, "ir_min_age": 61, "ir_rearrangement_file_name": "SRR030820_barcode68.txz", "ir_rearrangement_number": 259, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 249, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "9382", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 225 }, { "_id": 226, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-a ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5862", "cell_number": "635307", "ir_sequence_count": 5819, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode7.txz", "ir_rearrangement_number": 211, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 201, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5819", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 226 }, { "_id": 233, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_2", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_2-sc-2013-01-11T14:17:11Z-1548397", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "37532", "cell_number": "59088", "ir_sequence_count": 36726, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "62 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220446.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 62, "ir_min_age": 62, "ir_rearrangement_file_name": "ERR220446.txz", "ir_rearrangement_number": 382, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 372, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "36726", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 233 }, { "_id": 232, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "IgG+, CD19+, sIgG+, negative depletion to CD3, CD14, CD16, IgM, IgA, IgD ", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, lss8@columbia.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA188191", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "IAVI 84-Light Chain", "lab_name": "Kwong Lab", "pcr_target_locus": "IGL", "lab_address": "National Institute of Allergy and Infectious Disease-Vaccine Research Center", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS388604", "template_amount": null, "submitted_by": "P.D. Kwong, J. Zhu, G. Ofek", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "IAVI 84", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "873979", "cell_number": "973868", "ir_sequence_count": 873979, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "3 years", "template_class": "RNA", "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", "pub_ids": "PMID: 23536288", "disease_diagnosis": "HIV", "age": ">18 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IGLV", "ir_fasta_file_name": "filtered_SRR654170light_split1.fasta, filtered_SRR654170light_split2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 999, "ir_min_age": 18, "ir_rearrangement_file_name": "filtered_SRR654170light_split1.txz, filtered_SRR654170light_split2.txz", "ir_rearrangement_number": 2, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 2, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGLC", "ir_curator_count": "873979", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 232 }, { "_id": 231, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "11505", "cell_number": "270691", "ir_sequence_count": 11387, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode4.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode4.txz", "ir_rearrangement_number": 111, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 101, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "11387", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 231 }, { "_id": 234, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "55", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "55", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6217", "cell_number": "422073", "ir_sequence_count": 6097, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "55 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode60.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 55, "ir_min_age": 55, "ir_rearrangement_file_name": "SRR030820_barcode60.txz", "ir_rearrangement_number": 255, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 245, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6097", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 234 }, { "_id": 236, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_5-sc-2013-01-11T14:17:03Z-1548390", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2416", "cell_number": "2857", "ir_sequence_count": 2411, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220440.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220440.txz", "ir_rearrangement_number": 369, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 359, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "2411", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 236 }, { "_id": 238, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5000", "cell_number": "171714", "ir_sequence_count": 4969, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode1.txz", "ir_rearrangement_number": 144, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 134, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4969", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 238 }, { "_id": 242, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "60", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "60", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5621", "cell_number": "422073", "ir_sequence_count": 5527, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "60 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode61.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 60, "ir_min_age": 60, "ir_rearrangement_file_name": "SRR030820_barcode61.txz", "ir_rearrangement_number": 257, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 247, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5527", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 242 }, { "_id": 241, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_4-sc-2013-01-11T14:17:02Z-1548389", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3397", "cell_number": "3951", "ir_sequence_count": 3391, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220439.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220439.txz", "ir_rearrangement_number": 368, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 358, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3391", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 241 }, { "_id": 243, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "IgG+, CD19+, sIgG+, negative depletion to CD3, CD14, CD16, IgM, IgA, IgD ", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, lss8@columbia.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA188191", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "IAVI 84-Heavy Chain", "lab_name": "Kwong Lab", "pcr_target_locus": "IGH", "lab_address": "National Institute of Allergy and Infectious Disease-Vaccine Research Center", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS388604", "template_amount": null, "submitted_by": "P.D. Kwong, J. Zhu, G. Ofek", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "IAVI 84", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "253683", "cell_number": "279503", "ir_sequence_count": 253683, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "3 years", "template_class": "RNA", "study_title": "Mining the antibodyome for HIV-1 neutralizing antibodies with next generation sequencing and phylogenetic pairing of heavy/light chains", "pub_ids": "PMID: 23536288", "disease_diagnosis": "HIV", "age": ">18 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "filtered_SRR654169.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 999, "ir_min_age": 18, "ir_rearrangement_file_name": "filtered_SRR654169.txz", "ir_rearrangement_number": 1, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 1, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "253683", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 243 }, { "_id": 244, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_3-sc-2013-01-11T14:16:25Z-1548353", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9969", "cell_number": "11425", "ir_sequence_count": 9933, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220408.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220408.txz", "ir_rearrangement_number": 337, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 327, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9933", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 244 }, { "_id": 246, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "78", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "78", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5147", "cell_number": "433784", "ir_sequence_count": 5101, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "78 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode79.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 78, "ir_min_age": 78, "ir_rearrangement_file_name": "SRR030822_barcode79.txz", "ir_rearrangement_number": 268, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 258, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5101", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 246 }, { "_id": 249, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5355", "cell_number": "182564", "ir_sequence_count": 5336, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode1.txz", "ir_rearrangement_number": 143, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 133, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5336", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 249 }, { "_id": 248, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "37", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "37", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3531", "cell_number": "422073", "ir_sequence_count": 3480, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "37 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode37.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "SRR030820_barcode37.txz", "ir_rearrangement_number": 239, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 229, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3480", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 248 }, { "_id": 250, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_3-sc-2013-01-11T14:16:33Z-1548360", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6825", "cell_number": "7381", "ir_sequence_count": 6796, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220414.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220414.txz", "ir_rearrangement_number": 343, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 333, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6796", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 250 }, { "_id": 252, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9429", "cell_number": "270691", "ir_sequence_count": 9303, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode1.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode1.txz", "ir_rearrangement_number": 105, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 95, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "9303", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 252 }, { "_id": 253, "collapsing_method": null, "collection_time_point_relative": "sampled 2/5/2008", "sequencing_facility": null, "cell_phenotype": " CD3-, CD14-, CD19+, CD20+, IgG+, IgM-, RSC3+", "ethnicity": null, "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, jmascola@nih.gov", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA195543", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, igblast 1.8.0", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": "Antiretroviral", "data_processing_protocols": "Adaptors and primers removed and could not run igblast due to pooled light and heavy chains and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "IAVI 74", "lab_name": "Vaccine Research Center", "pcr_target_locus": "IGK", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS406328", "template_amount": null, "submitted_by": "T. Zhu, J. Zhou, P.D. Kwong, ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "IAVI 74", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1192320", "cell_number": "1300000", "ir_sequence_count": 1192320, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies", "pub_ids": "PMID: 23911655", "disease_diagnosis": "HIV", "age": ">18 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgVK3", "ir_fasta_file_name": "filtered_SRR800640heavyandlight_split1.fasta, filtered_SRR800640heavyandlight_split2.fasta, filtered_SRR800640heavyandlight_split3.fasta, unfiltered_SRR800640heavyandlight_split1.fasta, unfiltered_SRR800640heavyandlight_split2.fasta, unfiltered_SRR800640heavyandlight_split3.fasta", "ir_germline_database": "IMGT", "ir_library_source": null, "ir_max_age": 999, "ir_min_age": 18, "ir_rearrangement_file_name": "filtered_SRR800640heavyandlight_split1.txz, filtered_SRR800640heavyandlight_split2.txz, filtered_SRR800640heavyandlight_split3.txz", "ir_rearrangement_number": 20, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 10, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "IGKC", "ir_curator_count": "1192320", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 253 }, { "_id": 255, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_3-sc-2013-01-11T14:17:12Z-1548398", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "31224", "cell_number": "47363", "ir_sequence_count": 30559, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "75 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220447.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 75, "ir_min_age": 75, "ir_rearrangement_file_name": "ERR220447.txz", "ir_rearrangement_number": 383, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 373, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "30559", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 255 }, { "_id": 257, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "healthy donor 2-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "healthy donor 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6862", "cell_number": "182564", "ir_sequence_count": 6833, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode12.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode12.txz", "ir_rearrangement_number": 165, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 155, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6833", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 257 }, { "_id": 258, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 14 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5095", "cell_number": "171714", "ir_sequence_count": 5074, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode3.txz", "ir_rearrangement_number": 148, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 138, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5074", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 258 }, { "_id": 259, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "70", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "70", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6018", "cell_number": "422073", "ir_sequence_count": 5915, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "70 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode75.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 70, "ir_min_age": 70, "ir_rearrangement_file_name": "SRR030820_barcode75.txz", "ir_rearrangement_number": 263, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 253, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5915", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 259 }, { "_id": 260, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "unrelated CLL", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "unrelated CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8269", "cell_number": "635307", "ir_sequence_count": 8229, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode12.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode12.txz", "ir_rearrangement_number": 221, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 211, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8229", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 260 }, { "_id": 261, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Sibling, Mother", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Child B1", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033676", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Child B1", "intervention": null, "linked_subjects": "Child B2, Mother B", "total_reads_passing_qc_filter": "4830536", "cell_number": "4830536", "ir_sequence_count": 3873361, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "16 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "filtered_du_SRR1033676.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 16, "ir_min_age": 16, "ir_rearrangement_file_name": "SRR1033676_mixcr_annotation.txt", "ir_rearrangement_number": 272, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 262, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "3873361", "ir_ancillary_rearrangement_file_name": "SRR1033676_mixcr.vdjca, SRR1033676_mixcr_annotation.txt, SRR1033676_mixcr.clns, SRR1033676_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 261 }, { "_id": 263, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "31012_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619228", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "31012_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "162264", "cell_number": null, "ir_sequence_count": 161449, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "37 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298737.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "SRR1298737.txz", "ir_rearrangement_number": 413, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 403, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "161449", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 263 }, { "_id": 262, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 2 FL-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 2 FL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3124", "cell_number": "171714", "ir_sequence_count": 3112, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode7.txz", "ir_rearrangement_number": 156, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 146, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3112", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 262 }, { "_id": 264, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "31", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "31", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3037", "cell_number": "433784", "ir_sequence_count": 3004, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "31 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode31.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 31, "ir_min_age": 31, "ir_rearrangement_file_name": "SRR030822_barcode31.txz", "ir_rearrangement_number": 234, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 224, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3004", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 264 }, { "_id": 265, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3704", "cell_number": "171714", "ir_sequence_count": 3686, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode26.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode26.txz", "ir_rearrangement_number": 194, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 184, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3686", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 265 }, { "_id": 269, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "unrelated CLL", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "unrelated CLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7037", "cell_number": "556038", "ir_sequence_count": 7006, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode12.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode12.txz", "ir_rearrangement_number": 222, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 212, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7006", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 269 }, { "_id": 270, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Child, Child", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Mother A", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033671", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Mother A", "intervention": null, "linked_subjects": "Child A1, Child A2", "total_reads_passing_qc_filter": "13502141", "cell_number": "13656054", "ir_sequence_count": 12443081, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "36 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "SRR1033671_split_aa.fasta, SRR1033671_split_ab.fasta, SRR1033671_split_ac.fasta, SRR1033671_split_ad.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 36, "ir_min_age": 36, "ir_rearrangement_file_name": "SRR1033671_aa_mixcr_annotation.txt, SRR1033671_ab_mixcr_annotation.txt, SRR1033671_ac_mixcr_annotation.txt, SRR1033671_ad_mixcr_annotation.txt", "ir_rearrangement_number": 277, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 267, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "12443081", "ir_ancillary_rearrangement_file_name": "SRR1033671_aa_mixcr.vdjca, SRR1033671_aa_mixcr_annotation.txt, SRR1033671_ab_mixcr.vdjca, SRR1033671_ab_mixcr_annotation.txt, SRR1033671_ac_mixcr.vdjca, SRR1033671_ac_mixcr_annotation.txt, SRR1033671_ad_mixcr.vdjca, SRR1033671_ad_mixcr_annotation.txt, SRR1033671_aa_mixcr.clns, SRR1033671_aa_mixcr_clones.txt, SRR1033671_ab_mixcr.clns, SRR1033671_ab_mixcr_clones.txt, SRR1033671_ac_mixcr.clns, SRR1033671_ac_mixcr_clones.txt, SRR1033671_ad_mixcr.clns, SRR1033671_ad_mixcr_clones.txt", "paired_reads_assembly": "PEAR (Galaxy Version 0.9.6.0), Minimum possible length of the assembled sequences=60, Minimum length of reads after trimming the low quality part=60, Quality score threshold for triming the low quality part of a read=30, All else default values", "ir_project_sample_id": 270 }, { "_id": 271, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100000-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4279", "cell_number": "171714", "ir_sequence_count": 4243, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode19.txz", "ir_rearrangement_number": 180, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 170, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4243", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 271 }, { "_id": 272, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-f", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2757", "cell_number": "556038", "ir_sequence_count": 2738, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode6.txz", "ir_rearrangement_number": 210, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 200, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2738", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 272 }, { "_id": 274, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 3 FL and SLL-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 3 FL and SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "13937", "cell_number": "251408", "ir_sequence_count": 13875, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Small Lymphocytic Leukemia, Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode8.txz", "ir_rearrangement_number": 120, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 110, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "13875", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 274 }, { "_id": 276, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "16483", "cell_number": "270691", "ir_sequence_count": 16367, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode16.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode16.txz", "ir_rearrangement_number": 135, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 125, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "16367", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 276 }, { "_id": 279, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F4NCpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718548", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 4 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2485869", "cell_number": "3841175", "ir_sequence_count": 2485869, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "5 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875301.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 5, "ir_min_age": 5, "ir_rearrangement_file_name": "ERR875301_aa.txz, ERR875301_ab.txz, ERR875301_ac.txz, ERR875301_ad.txz, ERR875301_ae.txz", "ir_rearrangement_number": 433, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 423, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2485869", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875300_filtered_1.fastq -r ERR875300_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875300.fastq", "ir_project_sample_id": 279 }, { "_id": 282, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_13_barcode15", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_13_barcode15", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "37929", "cell_number": "72125", "ir_sequence_count": 37714, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode15.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode15.txz", "ir_rearrangement_number": 381, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 371, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "37714", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 282 }, { "_id": 284, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Liver tissue", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD liver DLBCL-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD liver DLBCL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3196", "cell_number": "171714", "ir_sequence_count": 3104, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode11.txz", "ir_rearrangement_number": 164, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 154, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3104", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 284 }, { "_id": 286, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_3-sc-2013-01-11T14:16:46Z-1548374", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5259", "cell_number": "6284", "ir_sequence_count": 5242, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220426.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220426.txz", "ir_rearrangement_number": 355, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 345, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5242", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 286 }, { "_id": 293, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-1a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1431", "cell_number": "270691", "ir_sequence_count": 1428, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode5.txz", "ir_rearrangement_number": 113, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 103, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1428", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 293 }, { "_id": 292, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "healthy donor 2-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "healthy donor 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6470", "cell_number": "171714", "ir_sequence_count": 6442, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode12.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode12.txz", "ir_rearrangement_number": 166, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 156, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6442", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 292 }, { "_id": 294, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Bone marrow", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD marrow infiltrate-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD marrow infiltrate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7715", "cell_number": "270691", "ir_sequence_count": 7635, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode10.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode10.txz", "ir_rearrangement_number": 123, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 113, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7635", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 294 }, { "_id": 296, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 3-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4888", "cell_number": "171714", "ir_sequence_count": 4865, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode14.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode14.txz", "ir_rearrangement_number": 170, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 160, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4865", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 296 }, { "_id": 299, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": " Healthy_12_barcode13", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": " Healthy_12_barcode13", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "22011", "cell_number": "32631", "ir_sequence_count": 21861, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode13.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode13.txz", "ir_rearrangement_number": 380, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 370, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "21861", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 299 }, { "_id": 302, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10000-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "17731", "cell_number": "270691", "ir_sequence_count": 17524, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode18.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode18.txz", "ir_rearrangement_number": 139, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 129, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "17524", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 302 }, { "_id": 301, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F3Cpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718545", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 3 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1394920", "cell_number": "3110161", "ir_sequence_count": 1394920, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "10 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875298.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 10, "ir_min_age": 10, "ir_rearrangement_file_name": "ERR875298_aa.txz, ERR875298_ab.txz, ERR875298_ac.txz", "ir_rearrangement_number": 436, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 426, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1394920", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875297_filtered_1.fastq -r ERR875297_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875297.fastq", "ir_project_sample_id": 301 }, { "_id": 303, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_2", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_2-sc-2013-01-11T14:16:16Z-1548345", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "31137", "cell_number": "52971", "ir_sequence_count": 30444, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "58 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220400.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 58, "ir_min_age": 58, "ir_rearrangement_file_name": "ERR220400.txz", "ir_rearrangement_number": 329, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 319, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "30444", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 303 }, { "_id": 306, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_5_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_5_8-sc-2013-01-11T14:17:29Z-1548417", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4899", "cell_number": "6173", "ir_sequence_count": 4833, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220465.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "ERR220465.txz", "ir_rearrangement_number": 401, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 391, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "4833", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 306 }, { "_id": 307, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:1000-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:1000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5993", "cell_number": "182564", "ir_sequence_count": 5955, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode17.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode17.txz", "ir_rearrangement_number": 175, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 165, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5955", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 307 }, { "_id": 308, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F1Cpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718536", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 1 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3111452", "cell_number": "4821880", "ir_sequence_count": 3111452, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "13 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875289.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 13, "ir_min_age": 13, "ir_rearrangement_file_name": "ERR875289_aa.txz, ERR875289_ab.txz, ERR875289_ac.txz, ERR875289_ad.txz, ERR875289_ae.txz, ERR875289_af.txz, ERR875289_ag.txz", "ir_rearrangement_number": 445, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 435, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "3111452", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 308 }, { "_id": 309, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_7-sc-2013-01-11T14:16:36Z-1548364", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5952", "cell_number": "6564", "ir_sequence_count": 5942, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220418.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220418.txz", "ir_rearrangement_number": 347, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 337, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5942", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 309 }, { "_id": 312, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_7-sc-2013-01-11T14:17:06Z-1548392", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6254", "cell_number": "6904", "ir_sequence_count": 6240, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220442.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220442.txz", "ir_rearrangement_number": 371, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 361, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6240", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 312 }, { "_id": 317, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F4NCpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718549", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 4 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1880567", "cell_number": "2997090", "ir_sequence_count": 1880567, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "5 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875302.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 5, "ir_min_age": 5, "ir_rearrangement_file_name": "ERR875302_aa.txz, ERR875302_ab.txz, ERR875302_ac.txz, ERR875302_ad.txz", "ir_rearrangement_number": 432, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 422, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1880567", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875301_filtered_1.fastq -r ERR875301_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875301.fastq", "ir_project_sample_id": 317 }, { "_id": 318, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3570", "cell_number": "182564", "ir_sequence_count": 3556, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode23.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode23.txz", "ir_rearrangement_number": 187, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 177, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3556", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 318 }, { "_id": 319, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_8-sc-2013-01-11T14:17:07Z-1548393", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3538", "cell_number": "4214", "ir_sequence_count": 3530, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220443.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220443.txz", "ir_rearrangement_number": 372, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 362, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3530", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 319 }, { "_id": 320, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 3 FL and SLL-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 3 FL and SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5279", "cell_number": "182564", "ir_sequence_count": 5261, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Small Lymphocytic Leukemia, Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode8.txz", "ir_rearrangement_number": 157, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 147, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5261", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 320 }, { "_id": 322, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_5_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_5_5-sc-2013-01-11T14:17:27Z-1548414", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3506", "cell_number": "4766", "ir_sequence_count": 3472, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220462.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "ERR220462.txz", "ir_rearrangement_number": 398, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 388, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3472", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 322 }, { "_id": 325, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4710", "cell_number": "182564", "ir_sequence_count": 4697, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode20.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode20.txz", "ir_rearrangement_number": 181, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 171, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4697", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 325 }, { "_id": 326, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4_6-sc-2013-01-11T14:17:21Z-1548408", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6688", "cell_number": "9217", "ir_sequence_count": 6604, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220457.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220457.txz", "ir_rearrangement_number": 393, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 383, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6604", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 326 }, { "_id": 327, "collapsing_method": null, "collection_time_point_relative": "Week 2 ", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A1wk2", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065378", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1463721", "cell_number": "2868249", "ir_sequence_count": 1463721, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "42 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278151.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 42, "ir_min_age": 42, "ir_rearrangement_file_name": "ERR1278151_aa.txz, ERR1278151_ab.txz, ERR1278151_ac.txz", "ir_rearrangement_number": 427, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 417, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1463721", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278151_filtered_1.fastq -r ERR1278151_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278151.fastq", "ir_project_sample_id": 327 }, { "_id": 331, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 3-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "17772", "cell_number": "270691", "ir_sequence_count": 17641, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode14.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode14.txz", "ir_rearrangement_number": 131, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 121, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "17641", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 331 }, { "_id": 335, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 1-1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 1 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3443", "cell_number": "182564", "ir_sequence_count": 3433, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode21.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode21.txz", "ir_rearrangement_number": 183, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 173, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3433", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 335 }, { "_id": 334, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3459", "cell_number": "182564", "ir_sequence_count": 3444, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode4.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode4.txz", "ir_rearrangement_number": 149, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 139, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3444", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 334 }, { "_id": 337, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Bone marrow", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 5 PTLD marrow infiltrate-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 5 PTLD marrow infiltrate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3721", "cell_number": "182564", "ir_sequence_count": 3710, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Diffuse Large B-cell Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode10.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode10.txz", "ir_rearrangement_number": 161, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 151, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3710", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 337 }, { "_id": 338, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Child, Child", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Mother C", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033673", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Mother C", "intervention": null, "linked_subjects": "Child C1, Child C2", "total_reads_passing_qc_filter": "10344067", "cell_number": "11167059", "ir_sequence_count": 10063432, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "43 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "SRR1033673_split_aa.fasta, SRR1033673_split_ab.fasta, SRR1033673_split_ac.fasta, SRR1033673_split_ad.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 43, "ir_min_age": 43, "ir_rearrangement_file_name": "SRR1033673_aa_mixcr_annotation.txt, SRR1033673_ab_mixcr_annotation.txt, SRR1033673_ac_mixcr_annotation.txt, SRR1033673_ad_mixcr_annotation.txt", "ir_rearrangement_number": 275, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 265, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "10063432", "ir_ancillary_rearrangement_file_name": "SRR1033673_aa_mixcr.vdjca, SRR1033673_aa_mixcr_annotation.txt, SRR1033673_ab_mixcr.vdjca, SRR1033673_ab_mixcr_annotation.txt, SRR1033673_ac_mixcr.vdjca, SRR1033673_ac_mixcr_annotation.txt, SRR1033673_ad_mixcr.vdjca, SRR1033673_ad_mixcr_annotation.txt, SRR1033673_aa_mixcr.clns, SRR1033673_aa_mixcr_clones.txt, SRR1033673_ab_mixcr.clns, SRR1033673_ab_mixcr_clones.txt, SRR1033673_ac_mixcr.clns, SRR1033673_ac_mixcr_clones.txt, SRR1033673_ad_mixcr.clns, SRR1033673_ad_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 338 }, { "_id": 339, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_8-sc-2013-01-11T14:16:52Z-1548379", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2160", "cell_number": "4569", "ir_sequence_count": 2154, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220431.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220431.txz", "ir_rearrangement_number": 360, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 350, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "2154", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 339 }, { "_id": 343, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Child, Child", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Mother B", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033672", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Mother B", "intervention": null, "linked_subjects": "Child B1, Child B2", "total_reads_passing_qc_filter": "11313287", "cell_number": "13872805", "ir_sequence_count": 10399769, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "43 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "SRR1033672_split_aa.fasta, SRR1033672_split_ab.fasta, SRR1033672_split_ac.fasta, SRR1033672_split_ad.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 43, "ir_min_age": 43, "ir_rearrangement_file_name": "SRR1033672_aa_mixcr_annotation.txt, SRR1033672_ab_mixcr_annotation.txt, SRR1033672_ac_mixcr_annotation.txt, SRR1033672_ad_mixcr_annotation.txt", "ir_rearrangement_number": 276, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 266, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "10399769", "ir_ancillary_rearrangement_file_name": "SRR1033672_aa_mixcr.vdjca, SRR1033672_aa_mixcr_annotation.txt, SRR1033672_ab_mixcr.vdjca, SRR1033672_ab_mixcr_annotation.txt, SRR1033672_ac_mixcr.vdjca, SRR1033672_ac_mixcr_annotation.txt, SRR1033672_ad_mixcr.vdjca, SRR1033672_ad_mixcr_annotation.txt, SRR1033672_aa_mixcr.clns, SRR1033672_aa_mixcr_clones.txt, SRR1033672_ab_mixcr.clns, SRR1033672_ab_mixcr_clones.txt, SRR1033672_ac_mixcr.clns, SRR1033672_ac_mixcr_clones.txt, SRR1033672_ad_mixcr.clns, SRR1033672_ad_mixcr_clones.txt", "paired_reads_assembly": "PEAR (Galaxy Version 0.9.6.0), Minimum possible length of the assembled sequences=60, Minimum length of reads after trimming the low quality part=60, Quality score threshold for triming the low quality part of a read=30, All else default values", "ir_project_sample_id": 343 }, { "_id": 349, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "50", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "50", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7211", "cell_number": "422073", "ir_sequence_count": 7083, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "50 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode54.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 50, "ir_min_age": 50, "ir_rearrangement_file_name": "SRR030820_barcode54.txz", "ir_rearrangement_number": 251, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 241, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7083", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 349 }, { "_id": 350, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_4-sc-2013-01-11T14:16:55Z-1548382", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5979", "cell_number": "8454", "ir_sequence_count": 5903, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220433.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220433.txz", "ir_rearrangement_number": 362, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 352, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5903", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 350 }, { "_id": 348, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "70", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "70", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6325", "cell_number": "433784", "ir_sequence_count": 6260, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "70 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode75.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 70, "ir_min_age": 70, "ir_rearrangement_file_name": "SRR030822_barcode75.txz", "ir_rearrangement_number": 264, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 254, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6260", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 348 }, { "_id": 353, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_10_barcode9", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_10_barcode9", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "40931", "cell_number": "58793", "ir_sequence_count": 40328, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode9.txz", "ir_rearrangement_number": 378, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 368, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "40328", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 353 }, { "_id": 352, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7743", "cell_number": "171714", "ir_sequence_count": 7699, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode15.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode15.txz", "ir_rearrangement_number": 172, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 162, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7699", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 352 }, { "_id": 354, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_7-sc-2013-01-11T14:16:29Z-1548357", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8647", "cell_number": "11091", "ir_sequence_count": 8641, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220412.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220412.txz", "ir_rearrangement_number": 341, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 331, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8641", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 354 }, { "_id": 356, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6183", "cell_number": "182564", "ir_sequence_count": 6159, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode5.txz", "ir_rearrangement_number": 151, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 141, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "6159", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 356 }, { "_id": 357, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3095", "cell_number": "171714", "ir_sequence_count": 3084, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode27.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode27.txz", "ir_rearrangement_number": 196, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 186, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3084", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 357 }, { "_id": 359, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "31", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "31", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2868", "cell_number": "422073", "ir_sequence_count": 2825, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "31 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode31.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 31, "ir_min_age": 31, "ir_rearrangement_file_name": "SRR030820_barcode31.txz", "ir_rearrangement_number": 233, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 223, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2825", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 359 }, { "_id": 360, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 14 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5307", "cell_number": "182564", "ir_sequence_count": 5278, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode3.txz", "ir_rearrangement_number": 147, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 137, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5278", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 360 }, { "_id": 361, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "42", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "42", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2482", "cell_number": "433784", "ir_sequence_count": 2451, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "42 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode44.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 42, "ir_min_age": 42, "ir_rearrangement_file_name": "SRR030822_barcode44.txz", "ir_rearrangement_number": 244, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 234, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2451", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 361 }, { "_id": 362, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4-sc-2013-01-11T14:17:13Z-1548399", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8703", "cell_number": "10646", "ir_sequence_count": 8540, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220448.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220448.txz", "ir_rearrangement_number": 384, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 374, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8540", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 362 }, { "_id": 365, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "32", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "32", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4134", "cell_number": "422073", "ir_sequence_count": 4066, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "32 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode32.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 32, "ir_min_age": 32, "ir_rearrangement_file_name": "SRR030820_barcode32.txz", "ir_rearrangement_number": 235, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 225, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4066", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 365 }, { "_id": 368, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F2NCpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718540", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 2 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3364283", "cell_number": "5891225", "ir_sequence_count": 3364283, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "14 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875293.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 14, "ir_min_age": 14, "ir_rearrangement_file_name": "ERR875293_aa.txz, ERR875293_ab.txz, ERR875293_ac.txz, ERR875293_ad.txz, ERR875293_ae.txz, ERR875293_af.txz, ERR875293_ag.txz", "ir_rearrangement_number": 441, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 431, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "3364283", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875292_filtered_1.fastq -r ERR875292_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875292.fastq", "ir_project_sample_id": 368 }, { "_id": 372, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_5-sc-2013-01-11T14:16:42Z-1548369", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6070", "cell_number": "9640", "ir_sequence_count": 6065, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220422.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220422.txz", "ir_rearrangement_number": 351, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 341, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6065", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 372 }, { "_id": 370, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F1NCpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718538", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 1 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4260441", "cell_number": "6353773", "ir_sequence_count": 4260441, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "11 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875291.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 11, "ir_min_age": 11, "ir_rearrangement_file_name": "ERR875291_aa.txz, ERR875291_ab.txz, ERR875291_ac.txz, ERR875291_ad.txz, ERR875291_ae.txz, ERR875291_af.txz, ERR875291_ag.txz, ERR875291_ah.txz, ERR875291_ai.txz", "ir_rearrangement_number": 443, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 433, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "4260441", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875290_filtered_1.fastq -r ERR875290_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875290.fastq", "ir_project_sample_id": 370 }, { "_id": 373, "collapsing_method": null, "collection_time_point_relative": "Week 2 ", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A3wk2", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065384", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1534270", "cell_number": "2563993", "ir_sequence_count": 1534270, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "47 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278157.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 47, "ir_min_age": 47, "ir_rearrangement_file_name": "ERR1278157_aa.txz, ERR1278157_ab.txz, ERR1278157_ac.txz, ERR1278157_ad.txz", "ir_rearrangement_number": 421, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 411, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1534270", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278157_filtered_1.fastq -r ERR1278157_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278157.fastq", "ir_project_sample_id": 373 }, { "_id": 375, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_8_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_8_5-sc-2013-01-11T14:16:57Z-1548383", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2452", "cell_number": "4458", "ir_sequence_count": 2538, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "64 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220434.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 64, "ir_min_age": 64, "ir_rearrangement_file_name": "ERR220434.txz", "ir_rearrangement_number": 363, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 353, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "2538", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 375 }, { "_id": 376, "collapsing_method": null, "collection_time_point_relative": "sampled 7/14/2006", "sequencing_facility": null, "cell_phenotype": " CD3-, CD14-, CD19+, CD20+, IgG+, IgM-, RSC3+", "ethnicity": "African", "sequencing_platform": "454 Roche GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pdkwong@nih.gov, jmascola@nih.gov", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": "Sample Collection", "medical_history": null, "disease_state_sample": "HIV+", "study_id": "PRJNA195543", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, igblast 1.8.0", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Adaptors and primers removed and igblast and imgt annotation of both quality filtered and unfiltered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "NIAID 45", "lab_name": "Vaccine Research Center", "pcr_target_locus": "IGK", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "HIV+ Study", "ir_sra_run_id": "SRS406329", "template_amount": null, "submitted_by": "T. Zhu, J. Zhou, P.D. Kwong, ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "15 million", "subject_id": "NIAID 45", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "663335", "cell_number": "740419", "ir_sequence_count": 663335, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": "23 years", "template_class": "RNA", "study_title": "Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies", "pub_ids": "PMID: 23911655", "disease_diagnosis": "HIV", "age": "56 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgVK3", "ir_fasta_file_name": "filtered_SRR800641kappa_split1.fasta, filtered_SRR800641kappa_split2.fasta, unfiltered_SRR800641kappa_split1.fasta, unfiltered_SRR800641kappa_split2.fasta", "ir_germline_database": "IMGT", "ir_library_source": null, "ir_max_age": 56, "ir_min_age": 56, "ir_rearrangement_file_name": "filtered_SRR800641kappa_split1.txz, filtered_SRR800641kappa_split2.txz", "ir_rearrangement_number": 16, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 6, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "IGKC", "ir_curator_count": "663335", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 376 }, { "_id": 378, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "23", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "23", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4866", "cell_number": "433784", "ir_sequence_count": 4819, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "23 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode23.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 23, "ir_min_age": 23, "ir_rearrangement_file_name": "SRR030822_barcode23.txz", "ir_rearrangement_number": 230, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 220, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4819", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 378 }, { "_id": 380, "collapsing_method": null, "collection_time_point_relative": "3 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-2-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1116", "cell_number": "251408", "ir_sequence_count": 1110, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode6.txz", "ir_rearrangement_number": 116, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 106, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1110", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 380 }, { "_id": 383, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_6-sc-2013-01-11T14:16:29Z-1548356", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8319", "cell_number": "10553", "ir_sequence_count": 8314, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220411.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220411.txz", "ir_rearrangement_number": 340, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 330, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8314", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 383 }, { "_id": 384, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_3-sc-2013-01-11T14:16:40Z-1548367", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9816", "cell_number": "11778", "ir_sequence_count": 9810, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220420.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220420.txz", "ir_rearrangement_number": 349, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 339, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9810", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 384 }, { "_id": 386, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-c ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3474", "cell_number": "556038", "ir_sequence_count": 3408, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode9.txz", "ir_rearrangement_number": 216, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 206, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3408", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 386 }, { "_id": 385, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "42", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "42", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2359", "cell_number": "422073", "ir_sequence_count": 2318, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "42 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode44.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 42, "ir_min_age": 42, "ir_rearrangement_file_name": "SRR030820_barcode44.txz", "ir_rearrangement_number": 243, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 233, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "2318", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 385 }, { "_id": 391, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4225", "cell_number": "171714", "ir_sequence_count": 4197, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode25.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode25.txz", "ir_rearrangement_number": 192, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 182, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4197", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 391 }, { "_id": 390, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "45a", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "45", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5473", "cell_number": "422073", "ir_sequence_count": 5389, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "45 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode45b.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 45, "ir_min_age": 45, "ir_rearrangement_file_name": "SRR030820_barcode45b.txz", "ir_rearrangement_number": 247, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 237, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5389", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 390 }, { "_id": 393, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F3NCpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718547", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 3 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2188780", "cell_number": "3008771", "ir_sequence_count": 2188780, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "4 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875300.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 4, "ir_min_age": 4, "ir_rearrangement_file_name": "ERR875300_aa.txz, ERR875300_ab.txz, ERR875300_ac.txz, ERR875300_ad.txz, ERR875300_ae.txz", "ir_rearrangement_number": 434, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 424, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2188780", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875299_filtered_1.fastq -r ERR875299_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875299.fastq", "ir_project_sample_id": 393 }, { "_id": 392, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "F1NCpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718539", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 1 Non-carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2904961", "cell_number": "4762812", "ir_sequence_count": 2904961, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "11 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875292.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 11, "ir_min_age": 11, "ir_rearrangement_file_name": "ERR875292_aa.txz, ERR875292_ab.txz, ERR875292_ac.txz, ERR875292_ad.txz, ERR875292_ae.txz, ERR875292_af.txz", "ir_rearrangement_number": 442, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 432, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2904961", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875291_filtered_1.fastq -r ERR875291_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875291.fastq", "ir_project_sample_id": 392 }, { "_id": 394, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_4-sc-2013-01-11T14:16:18Z-1548347", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "28254", "cell_number": "40641", "ir_sequence_count": 27592, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220402.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220402.txz", "ir_rearrangement_number": 331, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 321, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "27592", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 394 }, { "_id": 395, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "19", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "19", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "12985", "cell_number": "433784", "ir_sequence_count": 12855, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "19 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 19, "ir_min_age": 19, "ir_rearrangement_file_name": "SRR030822_barcode19.txz", "ir_rearrangement_number": 226, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 216, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "12855", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 395 }, { "_id": 396, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7-sc-2013-01-11T14:16:21Z-1548350", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5469", "cell_number": "7607", "ir_sequence_count": 5423, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220405.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220405.txz", "ir_rearrangement_number": 334, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 324, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5423", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 396 }, { "_id": 397, "collapsing_method": null, "collection_time_point_relative": "Day 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F4Cpost", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718551", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 4 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1784287", "cell_number": "2966573", "ir_sequence_count": 1784287, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "3 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875304.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 3, "ir_min_age": 3, "ir_rearrangement_file_name": "ERR875304_aa.txz, ERR875304_ab.txz, ERR875304_ac.txz, ERR875304_ad.txz", "ir_rearrangement_number": 430, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 420, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1784287", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875303_filtered_1.fastq -r ERR875303_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875303.fastq", "ir_project_sample_id": 397 }, { "_id": 398, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_10_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_10_4-sc-2013-01-11T14:16:26Z-1548354", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7430", "cell_number": "9405", "ir_sequence_count": 7415, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220409.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220409.txz", "ir_rearrangement_number": 338, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 328, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7415", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 398 }, { "_id": 400, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "25", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "25", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4227", "cell_number": "422073", "ir_sequence_count": 4169, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "25 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode25.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 25, "ir_min_age": 25, "ir_rearrangement_file_name": "SRR030820_barcode25.txz", "ir_rearrangement_number": 231, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 221, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4169", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 400 }, { "_id": 399, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_11_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_11_5-sc-2013-01-11T14:16:35Z-1548362", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2091", "cell_number": "2691", "ir_sequence_count": 2090, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "81 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220416.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 81, "ir_min_age": 81, "ir_rearrangement_file_name": "ERR220416.txz", "ir_rearrangement_number": 345, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 335, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "2090", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 399 }, { "_id": 401, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": "Caucasian", "sequencing_platform": "Illumina Hiseq 2000", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "chudakovdm@mail.ru", "link_type": "Sibling, Mother", "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJNA229070", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, MiXCR v2.1.10", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "All sequences annotated directly from the SRA files (the sequences were already de-multiplexed and quality was high enough) ---- Annotated through mixcr", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Child C2", "lab_name": "Shemyakin-Ovchinnikov institute of Bioorganic Chemistry ", "pcr_target_locus": "TRB", "lab_address": "Russian Academy of Sciences", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Healthy baseline Study", "ir_sra_run_id": "SRR1033679", "template_amount": null, "submitted_by": "E.V. Putintseva, O.V. Britanova, D.M. Chudakov", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Child C2", "intervention": null, "linked_subjects": "Child C1, Mother C", "total_reads_passing_qc_filter": "4564646", "cell_number": "4564646", "ir_sequence_count": 3701705, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Mother and child T cell receptor repertoires: deep profiling study", "pub_ids": "PMID: 24400004", "disease_diagnosis": "Healthy", "age": "16 years", "collection_time_point_reference": "Blood withdrawl", "forward_pcr_primer_target_location": "TRBV", "ir_fasta_file_name": "filtered_du_SRR1033679.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 16, "ir_min_age": 16, "ir_rearrangement_file_name": "SRR1033679_mixcr_annotation.txt", "ir_rearrangement_number": 269, "ir_rearrangement_tool": "MiXCR", "ir_record_number": 259, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "TRBJ, TRBC", "ir_curator_count": "3701705", "ir_ancillary_rearrangement_file_name": "SRR1033679_mixcr.vdjca, SRR1033679_mixcr_annotation.txt, SRR1033679_mixcr.clns, SRR1033679_mixcr_clones.txt", "paired_reads_assembly": null, "ir_project_sample_id": 401 }, { "_id": 403, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_6-sc-2013-01-11T14:16:43Z-1548370", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8770", "cell_number": "11197", "ir_sequence_count": 8761, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220423.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220423.txz", "ir_rearrangement_number": 352, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 342, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "8761", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 403 }, { "_id": 406, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100000-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "16384", "cell_number": "251408", "ir_sequence_count": 16113, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode19.txz", "ir_rearrangement_number": 142, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 132, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "16113", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 406 }, { "_id": 407, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "54", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "54", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5768", "cell_number": "422073", "ir_sequence_count": 5645, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "54 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode55.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 54, "ir_min_age": 54, "ir_rearrangement_file_name": "SRR030820_barcode55.txz", "ir_rearrangement_number": 253, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 243, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5645", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 407 }, { "_id": 408, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-b ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4842", "cell_number": "635307", "ir_sequence_count": 4805, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode8.txz", "ir_rearrangement_number": 213, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 203, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4805", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 408 }, { "_id": 409, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-d", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1816", "cell_number": "556038", "ir_sequence_count": 1807, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode4.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode4.txz", "ir_rearrangement_number": 206, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 196, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1807", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 409 }, { "_id": 410, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_6-sc-2013-01-11T14:16:50Z-1548377", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3352", "cell_number": "4878", "ir_sequence_count": 3312, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220429.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220429.txz", "ir_rearrangement_number": 358, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 348, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3312", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 410 }, { "_id": 411, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-b ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4254", "cell_number": "556038", "ir_sequence_count": 4211, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode8.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode8.txz", "ir_rearrangement_number": 214, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 204, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4211", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 411 }, { "_id": 413, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "45b", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "45", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5028", "cell_number": "422073", "ir_sequence_count": 4950, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "45 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode50.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 45, "ir_min_age": 45, "ir_rearrangement_file_name": "SRR030820_barcode50.txz", "ir_rearrangement_number": 249, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 239, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4950", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 413 }, { "_id": 414, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Hepatitis B", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "F3Cpre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS718544", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Family 3 Carrier", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3400216", "cell_number": "4490360", "ir_sequence_count": 3400216, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Hepatitis B", "age": "10 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR875297.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 10, "ir_min_age": 10, "ir_rearrangement_file_name": "ERR875297_aa.txz, ERR875297_ab.txz, ERR875297_ac.txz, ERR875297_ad.txz, ERR875297_ae.txz, ERR875297_af.txz, ERR875297_ag.txz", "ir_rearrangement_number": 437, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 427, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "3400216", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR875296_filtered_1.fastq -r ERR875296_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR875296.fastq", "ir_project_sample_id": 414 }, { "_id": 415, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:10000-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:10000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5373", "cell_number": "171714", "ir_sequence_count": 5350, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode18.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode18.txz", "ir_rearrangement_number": 178, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 168, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5350", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 415 }, { "_id": 416, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4_5-sc-2013-01-11T14:17:20Z-1548407", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3413", "cell_number": "5291", "ir_sequence_count": 3366, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220456.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220456.txz", "ir_rearrangement_number": 392, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 382, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "3366", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 416 }, { "_id": 418, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "35", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "35", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3765", "cell_number": "433784", "ir_sequence_count": 3726, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "35 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode35.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 35, "ir_min_age": 35, "ir_rearrangement_file_name": "SRR030822_barcode35.txz", "ir_rearrangement_number": 238, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 228, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3726", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 418 }, { "_id": 419, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "35", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "35", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3690", "cell_number": "422073", "ir_sequence_count": 3621, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "35 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode35.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 35, "ir_min_age": 35, "ir_rearrangement_file_name": "SRR030820_barcode35.txz", "ir_rearrangement_number": 237, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 227, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3621", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 419 }, { "_id": 423, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4_8-sc-2013-01-11T14:17:23Z-1548410", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5546", "cell_number": "7468", "ir_sequence_count": 5462, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220459.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220459.txz", "ir_rearrangement_number": 395, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 385, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5462", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 423 }, { "_id": 429, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_13_barcode7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_13_barcode7", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "124793", "cell_number": "211723", "ir_sequence_count": 123281, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode7.txz", "ir_rearrangement_number": 377, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 367, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "123281", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 429 }, { "_id": 430, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "14711_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619113", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "14711_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "142558", "cell_number": null, "ir_sequence_count": 141696, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "20 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298730.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 20, "ir_min_age": 20, "ir_rearrangement_file_name": "SRR1298730.txz", "ir_rearrangement_number": 416, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 406, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "141696", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 430 }, { "_id": 431, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-e ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3085", "cell_number": "556038", "ir_sequence_count": 3039, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode11.txz", "ir_rearrangement_number": 220, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 210, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3039", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 431 }, { "_id": 432, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-e ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3378", "cell_number": "635307", "ir_sequence_count": 3332, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode11.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode11.txz", "ir_rearrangement_number": 219, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 209, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3332", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 432 }, { "_id": 434, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "50", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "50", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7240", "cell_number": "433784", "ir_sequence_count": 7168, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "50 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode54.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 50, "ir_min_age": 50, "ir_rearrangement_file_name": "SRR030822_barcode54.txz", "ir_rearrangement_number": 252, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 242, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "7168", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 434 }, { "_id": 435, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-c", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3547", "cell_number": "635307", "ir_sequence_count": 3534, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode3.txz", "ir_rearrangement_number": 203, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 193, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3534", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 435 }, { "_id": 436, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:1000-b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:1000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5751", "cell_number": "171714", "ir_sequence_count": 5711, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode17.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode17.txz", "ir_rearrangement_number": 176, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 166, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5711", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 436 }, { "_id": 437, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3c2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3952", "cell_number": "171714", "ir_sequence_count": 3930, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode28.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode28.txz", "ir_rearrangement_number": 198, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 188, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3930", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 437 }, { "_id": 439, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100000-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4558", "cell_number": "182564", "ir_sequence_count": 4536, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode19.txz", "ir_rearrangement_number": 179, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 169, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4536", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 439 }, { "_id": 440, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "45a", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "45", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5311", "cell_number": "433784", "ir_sequence_count": 5265, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "45 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode45b.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 45, "ir_min_age": 45, "ir_rearrangement_file_name": "SRR030822_barcode45b.txz", "ir_rearrangement_number": 248, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 238, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5265", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 440 }, { "_id": 442, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_5_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_5_4-sc-2013-01-11T14:17:26Z-1548413", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5619", "cell_number": "6826", "ir_sequence_count": 5526, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220461.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "ERR220461.txz", "ir_rearrangement_number": 397, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 387, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5526", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 442 }, { "_id": 446, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "30512_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619239", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "30512_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "18009", "cell_number": null, "ir_sequence_count": 17960, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "34 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298734.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 34, "ir_min_age": 34, "ir_rearrangement_file_name": "SRR1298734.txz", "ir_rearrangement_number": 406, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 396, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "17960", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 446 }, { "_id": 447, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 4 CLL/SLL-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 4 CLL/SLL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "17999", "cell_number": "251408", "ir_sequence_count": 17811, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode9.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode9.txz", "ir_rearrangement_number": 122, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 112, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "17811", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 447 }, { "_id": 449, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL B-d ", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL B ", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3145", "cell_number": "556038", "ir_sequence_count": 3033, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030817_filtered_barcode10.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030817_barcode10.txz", "ir_rearrangement_number": 218, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 208, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3033", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 449 }, { "_id": 452, "collapsing_method": null, "collection_time_point_relative": "3 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-2a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1196", "cell_number": "270691", "ir_sequence_count": 1194, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode6.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode6.txz", "ir_rearrangement_number": 115, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 105, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1194", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 452 }, { "_id": 453, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100000-a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100000", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "17595", "cell_number": "270691", "ir_sequence_count": 17355, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030807_filtered_barcode19.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030807_barcode19.txz", "ir_rearrangement_number": 141, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 131, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "17355", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 453 }, { "_id": 455, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9_6", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9_6-sc-2013-01-11T14:17:04Z-1548391", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5042", "cell_number": "5576", "ir_sequence_count": 5034, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220441.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220441.txz", "ir_rearrangement_number": 370, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 360, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "5034", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 455 }, { "_id": 454, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1 time 0 replicate", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4659", "cell_number": "182564", "ir_sequence_count": 4645, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode2.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode2.txz", "ir_rearrangement_number": 145, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 135, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4645", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 454 }, { "_id": 456, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_9", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_9-sc-2013-01-11T14:16:24Z-1548352", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "6779", "cell_number": "7427", "ir_sequence_count": 6766, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "77 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220407.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 77, "ir_min_age": 77, "ir_rearrangement_file_name": "ERR220407.txz", "ir_rearrangement_number": 336, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 326, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "6766", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 456 }, { "_id": 457, "collapsing_method": null, "collection_time_point_relative": "Week 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A3wk1", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065383", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 3", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2148806", "cell_number": "2408132", "ir_sequence_count": 2148806, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "47 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278156.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 47, "ir_min_age": 47, "ir_rearrangement_file_name": "ERR1278156_aa.txz, ERR1278156_ab.txz, ERR1278156_ac.txz, ERR1278156_ad.txz, ERR1278156_ae.txz", "ir_rearrangement_number": 422, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 412, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "2148806", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278156_filtered_1.fastq -r ERR1278156_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278156.fastq", "ir_project_sample_id": 457 }, { "_id": 459, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_12_barcode5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_12_barcode5", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "42922", "cell_number": "66266", "ir_sequence_count": 42410, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "24 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220445.barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 24, "ir_min_age": 24, "ir_rearrangement_file_name": "ERR220445_barcode5.txz", "ir_rearrangement_number": 376, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 366, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "42410", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 459 }, { "_id": 463, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_6_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_6_8-sc-2013-01-11T14:16:45Z-1548372", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "7369", "cell_number": "9567", "ir_sequence_count": 7347, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220425.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220425.txz", "ir_rearrangement_number": 354, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 344, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "7347", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 463 }, { "_id": 467, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "68", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "68", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "8297", "cell_number": "433784", "ir_sequence_count": 8198, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "68 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode70.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 68, "ir_min_age": 68, "ir_rearrangement_file_name": "SRR030822_barcode70.txz", "ir_rearrangement_number": 262, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 252, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "8198", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 467 }, { "_id": 468, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "43113_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619242", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "43113_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5876", "cell_number": null, "ir_sequence_count": 5840, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "31 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298740.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 31, "ir_min_age": 31, "ir_rearrangement_file_name": "SRR1298740.txz", "ir_rearrangement_number": 403, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 393, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "5840", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 468 }, { "_id": 469, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Diagnostic lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": "Total lymphoid irradiation, antithymocyte glboun therapy followed by HLA-identical allogenic peripheral progenitor cell blood transplantation", "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL A-e", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007524", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "CLL A", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1145", "cell_number": "635307", "ir_sequence_count": 1141, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030816_filtered_barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030816_barcode5.txz", "ir_rearrangement_number": 207, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 197, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "1141", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 469 }, { "_id": 470, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 6 CLL diluted 1:100-a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 6 CLL diluted 1:100", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5449", "cell_number": "182564", "ir_sequence_count": 5424, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode16.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode16.txz", "ir_rearrangement_number": 173, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 163, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5424", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 470 }, { "_id": 471, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_8", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_8-sc-2013-01-11T14:17:17Z-1548403", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "27675", "cell_number": "40467", "ir_sequence_count": 27102, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "23 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220452.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 23, "ir_min_age": 23, "ir_rearrangement_file_name": "ERR220452.txz", "ir_rearrangement_number": 388, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 378, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "27102", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 471 }, { "_id": 472, "collapsing_method": null, "collection_time_point_relative": "Week 1", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A4wk1", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065386", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 4", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1493227", "cell_number": "2820131", "ir_sequence_count": 1493227, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "37 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278159.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "ERR1278159_aa.txz, ERR1278159_ab.txz, ERR1278159_ac.txz", "ir_rearrangement_number": 419, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 409, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1493227", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278159_filtered_1.fastq -r ERR1278159_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278159.fastq", "ir_project_sample_id": 472 }, { "_id": 473, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_9", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_9-sc-2013-01-11T14:17:18Z-1548404", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "18311", "cell_number": "29786", "ir_sequence_count": 18101, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "25 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220453.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 25, "ir_min_age": 25, "ir_rearrangement_file_name": "ERR220453.txz", "ir_rearrangement_number": 389, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 379, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "18101", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 473 }, { "_id": 475, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "14711_CSF", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619233", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "14711_CSF", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "20617", "cell_number": null, "ir_sequence_count": 20488, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "20 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298731.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 20, "ir_min_age": 20, "ir_rearrangement_file_name": "SRR1298731.txz", "ir_rearrangement_number": 409, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 399, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "20488", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 475 }, { "_id": 476, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A4pre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065385", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 4", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1420729", "cell_number": "2041832", "ir_sequence_count": 1420729, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "37 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278158.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 37, "ir_min_age": 37, "ir_rearrangement_file_name": "ERR1278158_aa.txz, ERR1278158_ab.txz, ERR1278158_ac.txz", "ir_rearrangement_number": 420, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 410, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1420729", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278158_filtered_1.fastq -r ERR1278158_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278158.fastq", "ir_project_sample_id": 476 }, { "_id": 480, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4061", "cell_number": "171714", "ir_sequence_count": 4040, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode24.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode24.txz", "ir_rearrangement_number": 190, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 180, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4040", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 480 }, { "_id": 481, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 3a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 14 months", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3935", "cell_number": "182564", "ir_sequence_count": 3919, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode26.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode26.txz", "ir_rearrangement_number": 193, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 183, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "3919", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 481 }, { "_id": 483, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": "CD19, IgD, CD27", "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "Hans-Christian.vonBuedingen@ucsf.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Multiple Sclerosis", "study_id": "PRJNA248411", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "43113_PBMC", "lab_name": "Von Budingen Lab", "pcr_target_locus": "IGH", "lab_address": "University of California San Francisco (UCSF)", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Multiple Sclerosis Study", "ir_sra_run_id": "SRS619230", "template_amount": null, "submitted_by": "Palanichamy, Apeltsin et al ", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^9", "subject_id": "43113_PBMC", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "179282", "cell_number": null, "ir_sequence_count": 177810, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis", "pub_ids": "PMID: 25100740", "disease_diagnosis": "Multiple Sclerosis", "age": "31 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "IgM-VH, IgG-VH", "ir_fasta_file_name": "filtered_SRR1298741.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 31, "ir_min_age": 31, "ir_rearrangement_file_name": "SRR1298741.txz", "ir_rearrangement_number": 411, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 401, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IgG, IgM isotype specific reverse primers", "ir_curator_count": "177810", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 483 }, { "_id": 484, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A2pre", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065379", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1581000", "cell_number": "3894726", "ir_sequence_count": 1581000, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "35 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278152.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 35, "ir_min_age": 35, "ir_rearrangement_file_name": "ERR1278152_aa.txz, ERR1278152_ab.txz, ERR1278152_ac.txz, ERR1278152_ad.txz", "ir_rearrangement_number": 426, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 416, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "1581000", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278152_filtered_1.fastq -r ERR1278152_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278152.fastq", "ir_project_sample_id": 484 }, { "_id": 485, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_4", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_4-sc-2013-01-11T14:16:48Z-1548375", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "2407", "cell_number": "4864", "ir_sequence_count": 2393, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220427.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220427.txz", "ir_rearrangement_number": 356, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 346, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "2393", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 485 }, { "_id": 486, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_7", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_7-sc-2013-01-11T14:17:16Z-1548402", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "21389", "cell_number": "31957", "ir_sequence_count": 20917, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "23 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220451.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 23, "ir_min_age": 23, "ir_rearrangement_file_name": "ERR220451.txz", "ir_rearrangement_number": 387, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 377, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "20917", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 486 }, { "_id": 489, "collapsing_method": null, "collection_time_point_relative": "Week 2 ", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "Illumina NextSeq", "cell_subset": "Plasma cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "hhliu@nhri.org.tw)", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB9332", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.11", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "A2wk2", "lab_name": "Institute of Molecular and Genomic Medicine, National Health Research Institutes", "pcr_target_locus": "IGH", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Hepatitis B Study", "ir_sra_run_id": "ERS1065381", "template_amount": null, "submitted_by": "Chang, Y.H., Kuan, H.C.", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Adult 2", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "3199488", "cell_number": "5123678", "ir_sequence_count": 3199488, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses.", "pub_ids": "PMID: 27222149", "disease_diagnosis": "Healthy", "age": "35 years", "collection_time_point_reference": "Vaccination", "forward_pcr_primer_target_location": "IGHV", "ir_fasta_file_name": "paired_ERR1278154.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Transcriptomic", "ir_max_age": 35, "ir_min_age": 35, "ir_rearrangement_file_name": "ERR1278154_aa.txz, ERR1278154_ab.txz, ERR1278154_ac.txz, ERR1278154_ad.txz, ERR1278154_ae.txz, ERR1278154_af.txz, ERR1278154_ag.txz", "ir_rearrangement_number": 424, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 414, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHC", "ir_curator_count": "3199488", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": "pear -f ERR1278154_filtered_1.fastq -r ERR1278154_filtered_2.fastq -n 60 -t 60 -q 25 -o paired_ERR1278154.fastq", "ir_project_sample_id": 489 }, { "_id": 490, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 1 CLL/SLL-1b2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 1 CLL/SLL time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5799", "cell_number": "171714", "ir_sequence_count": 5769, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Chronic Lymphocytic Leukemia/Small Lymphocytic Leukemia", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030815_filtered_barcode5.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030815_barcode5.txz", "ir_rearrangement_number": 152, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 142, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5769", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 490 }, { "_id": 491, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy_4_3", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "Healthy_4_3-sc-2013-01-11T14:17:18Z-1548405", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9320", "cell_number": "11092", "ir_sequence_count": 9173, "physical_linkage": null, "sex": "Female", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Healthy", "age": "67 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220454.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 67, "ir_min_age": 67, "ir_rearrangement_file_name": "ERR220454.txz", "ir_rearrangement_number": 390, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 380, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "9173", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 491 }, { "_id": 493, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "B cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Lymph node", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Lymphoma", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "Patient 2 FL-b1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Patient 2 FL", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "5585", "cell_number": "251408", "ir_sequence_count": 5554, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Follicular Lymphoma", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode7.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode7.txz", "ir_rearrangement_number": 118, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 108, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "5554", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 493 }, { "_id": 495, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "61", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "61", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "9806", "cell_number": "433784", "ir_sequence_count": 9693, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "61 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030822_filtered_barcode68.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 61, "ir_min_age": 61, "ir_rearrangement_file_name": "SRR030822_barcode68.txz", "ir_rearrangement_number": 260, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 250, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "9693", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 495 }, { "_id": 496, "collapsing_method": null, "collection_time_point_relative": "Day 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Experiment 2 Healthy donor 2 1a2", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007523", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Exp2 only Healthy donor 2 time 0", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4346", "cell_number": "182564", "ir_sequence_count": 4319, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030813_filtered_barcode24.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030813_barcode24.txz", "ir_rearrangement_number": 189, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 179, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4319", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 496 }, { "_id": 499, "collapsing_method": null, "collection_time_point_relative": "Day 0 and 14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": null, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "23", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007525", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "23", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "4696", "cell_number": "422073", "ir_sequence_count": 4617, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": "23 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": " SRR030820_filtered_barcode23.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 23, "ir_min_age": 23, "ir_rearrangement_file_name": "SRR030820_barcode23.txz", "ir_rearrangement_number": 229, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 219, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "4617", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 499 }, { "_id": 501, "collapsing_method": null, "collection_time_point_relative": "14 months", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Healthy", "study_id": "SRP001460", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.3", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 25, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast and imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Control", "sample_id": "Healthy donor 1-3a1", "lab_name": "Department of Pathology, Stanford University", "pcr_target_locus": "IGH", "lab_address": "Stanford University", "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "SRS007513", "template_amount": null, "submitted_by": "Boyd S.D, Marshall E.L ", "read_length": null, "ancestry_population": null, "cells_per_reaction": null, "subject_id": "Healthy donor 1", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "11830", "cell_number": "251408", "ir_sequence_count": 11689, "physical_linkage": null, "sex": null, "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "DNA", "study_title": "Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing", "pub_ids": "PMID: 20161664", "disease_diagnosis": "Healthy", "age": null, "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "SRR030809_filtered_barcode3.fasta", "ir_germline_database": "IMGT", "ir_library_source": "genomic", "ir_max_age": 999, "ir_min_age": -1, "ir_rearrangement_file_name": "SRR030809_barcode3.txz", "ir_rearrangement_number": 110, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 100, "library_generation_method": "PCR", "reverse_pcr_primer_target_location": "IGHJ", "ir_curator_count": "11689", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 501 }, { "_id": 500, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX Titanium", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "pk5@sanger.ac.uk", "link_type": null, "immunogen": null, "cell_storage": null, "age_event": null, "medical_history": null, "disease_state_sample": "Chronic Lymphocytic Leukemia", "study_id": "PRJEB1289", "sequencing_run_date": null, "grants": null, "single_cell": 0, "software_versions": "SRA Toolkit 2.8.2-1, cutadapt 1.14, fastqc 0.11.5, pear 0.9.10, biopython 2.7.13, IMGT/V-QUEST 3.4.8", "template_quality": null, "race": null, "cell_isolation": null, "tissue_processing": null, "quality_thresholds": 30, "prior_therapies": null, "data_processing_protocols": "Barcodes and primers removed and igblast/imgt annotation of quality filtered sequences", "library_generation_protocol": null, "biomaterial_provider": null, "disease_stage": null, "study_group_description": "Case", "sample_id": "CLL_7_5", "lab_name": "The Wellcome Trust Sanger Institute", "pcr_target_locus": "TRB", "lab_address": null, "sequencing_run_id": null, "primer_match_cutoffs": null, "anatomic_site": null, "complete_sequences": "partial", "strain_name": null, "library_generation_kit_version": null, "cell_quality": null, "cell_processing_protocol": null, "study_description": "Cancer Study", "ir_sra_run_id": "ERS205713", "template_amount": null, "submitted_by": "Bashford-Rogers, Palser", "read_length": null, "ancestry_population": null, "cells_per_reaction": "1*10^6", "subject_id": "CLL_7_5-sc-2013-01-11T14:16:49Z-1548376", "intervention": null, "linked_subjects": null, "total_reads_passing_qc_filter": "1180", "cell_number": "2576", "ir_sequence_count": 1157, "physical_linkage": null, "sex": "Male", "synthetic": 0, "inclusion_exclusion_criteria": null, "sample_type": null, "disease_length": null, "template_class": "RNA", "study_title": "Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations", "pub_ids": "PMID: 23742949", "disease_diagnosis": "Chronic Lymphocytic Leukemia", "age": "69 years", "collection_time_point_reference": "Sample collection", "forward_pcr_primer_target_location": "FR1 and FR2", "ir_fasta_file_name": "filtered_ERR220428.fasta", "ir_germline_database": "IMGT", "ir_library_source": "Genomic", "ir_max_age": 69, "ir_min_age": 69, "ir_rearrangement_file_name": "ERR220428.txz", "ir_rearrangement_number": 357, "ir_rearrangement_tool": "IMGT high-Vquest", "ir_record_number": 347, "library_generation_method": "Other", "reverse_pcr_primer_target_location": "TRBJ ", "ir_curator_count": "1157", "ir_ancillary_rearrangement_file_name": null, "paired_reads_assembly": null, "ir_project_sample_id": 500 }, { "_id": 503, "collapsing_method": null, "collection_time_point_relative": "Time 0", "sequencing_facility": null, "cell_phenotype": null, "ethnicity": null, "sequencing_platform": "454 GS FLX", "cell_subset": "Peripheral blood mononuclear cells", "sequencing_kit": null, "organism": "Homo sapiens", "tissue": "Blood", "collected_by": "afire@stanford.edu", "link_type": null, "immunogen": null, "ce