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Publicly available AIRR-seq data sets: B cells

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This page holds a list of B-cell papers for which there are publicly available AIRR-seq data. By publicly available we mean data that is available via an open data platform (such as the INSDC repositories - SRA/ENA) or data sharing agreement. The page provides links to the papers and the sources for the sequence data (SRA, ENA, etc.). If annotated AIRR-seq data are available, links for those data sets are provided (e.g. iReceptor, ImmunoAccess, Observer Antibody Space, VDJServer, etc.). There are a number of related pages on b-t.cr that contain further paper references, as listed below:

If you know of others, please add them!

B Cell papers with data sets:

  1. Banerjee, S. et al. Evaluation of a novel multi-immunogen vaccine strategy for targeting 4E10/10E8 neutralizing epitopes on HIV-1 gp41 membrane proximal external region. Virology 505:113-26 (2017).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA355270
    • Species: Oryctolagus cuniculus (Rabbit)
    • Illumina MiSeq 2x250, mRNA
  2. Bashford-Rogers, R.J. et al. Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations. Genome Res 23:1874–84 (2013).
    [DOI] [PubMed] [PMC]
    • ENA Study: PRJEB1289, ERP002120
    • Species: Homo sapiens
    • Roche 454, mRNA
    • The publication also states Illumina MiSeq 2x250, but cannot locate this data.
    • Annotated sequences available on iReceptor
  3. Bhiman, J.N. et al. Viral variant that initiate and drive maturation of VIV2-directed HIV-1 broadly neutralising antibodies. Nat Med. 21(11):1332 (2015).
    [DOI] [PubMed]
  4. Bolland, D.J. et al. Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Rep 15:2475-87 (2016).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA318060
    • Species: Mus musculus
    • Illumina HiSeq 1000, gDNA
  5. Boisvert, M. et al. Novel E2 glycoprotein tetramer detects HCV-specific memory B cells. J. Immunol. 197(12):4848-4858 (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
  6. Bonsignori, M. et al. Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell 165:449-63 (2016).
    [DOI] [PubMed] [PMC]
  7. Boyd, S.D. et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med 1:12ra23 (2009).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP001460
    • Species: Homo sapiens
    • Roche 454, gDNA
    • Annotated sequences available on iReceptor
  8. Briney, B. et al. Commonality despite exceptional diversity in the baseline human antibody repertoire. Nature, 566, 393-97 (2019).
    [DOI]
    • SRA Accession: PRJNA406949
    • Species: Homo sapiens
    • Illumina HiSeq 2500, mRNA
    • Annotated sequences available on VDJServer
  9. Chang, Y.-H. et al. Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses. Sci. Rep. 6, 26556 (2016).
    [DOI] [PubMed] [PMC]
    • ENA Accession: PRJEB9332
    • Species: Homo sapiens
    • Illumina NextSeq 2x150, mRNA
    • Annotated sequences available on iReceptor
  10. Chen, Y. et al. Microbial symbionts regulate the primary Ig repertoire. Jem 1761(2018).
    [DOI] [PubMed]
  11. Cole, C. et al. Highly Accurate Sequencing of Full-length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier-Guided Amplicon Assembly. J Immunol. 196: 6 2902-2907 (2016).
    [DOI] [PubMed]
    • SRA Accession: SRP061676
    • Species: Homo Sapiens
    • Illumina HiSeq 3000, mRNA
  12. Collins, A.M. et al. The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140236 (2015).
    [DOI] [PubMed] [PMC]
    • ENA Accession: PRJEB8745
    • Species: Mus musculus
    • Roche 454, mRNA
    • Annotated sequences available on iReceptor
  13. Corcoran, M.M. et al. Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Nat. Commun. 7, 13642 (2016).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJEB15295
    • Species: Homo Sapiens, Macaca mulatta, Mus musculus
    • MiSeq 2x300bp, mRNA
  14. Cui, A. et al. A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data. J. Immunol. 197, 3566–3574 (2016).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA283640
    • Species: Mus musculus
    • Illumina MiSeq 2x300, mRNA, 5’RACE, 17bp UMI
    • Annotated sequences available at VDJServer
  15. de Bourcy, C. et al. Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. Science Immunology, 2(15) (2017).
    [DOI] [PubMed]
  16. DeKosky, B.J. et al. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nature Biotechnology. 31(2):166-169 (2013).
    [DOI]
    • SRA Accession: SRA061316
    • Illumina MiSeq 2x250, single cell emulsion PCR-linked heavy and light chain
  17. DeKosky, B.J. et al. In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire. Nature Medicine. 21(1):86-91 (2015).
    [DOI]
    • SRA Accession: SRP047462
    • Illumina MiSeq 2x250, single cell emulsion PCR-linked heavy and light chain
    • Annotated sequences available on iReceptor
    • Annotated sequences available on VDJServer
  18. DeKosky, B.J. et al. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. PNAS 2016 May 10;113(19):E2636-45.
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA315079
    • Single cell emulsion PCR-linked heavy and light chain
    • Annotated sequences available on VDJServer
  19. DeWitt, W.S. et al. Dynamics of the cytotoxic T cell response to a model of acute viral infection. J. Virol. 2015 Apr;89(8):4517-26.
    [DOI]
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
    • Annotated sequences available on VDJServer
  20. DeWitt, W.S. et al. A public database of memory and naive B-cell receptor sequences. PLoS ONE 11(8): e0160853 (2016).
    [DOI]
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
    • Annotated sequences available on VDJServer
  21. Doria-Rose, N. et al. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. 509(7498):55-62 (2014).
    [DOI] [PubMed]
    • SRA Accessions: SRP034555, SRP017087
    • Roche 454, mRNA, mostly VH3- and VK- specific multiplex primers.
  22. Doria-Rose, N.A. et al. New member of the V1V2 directed CAP256-VRC26 lineage that shows increased breadth and exceptional potency. J. Virol. 90:1, 76 (2015).
    [DOI] [PubMed]
  23. Eggers, E.L. et al. Clonal relationships of CSF B cells in treatment-naïve multiple sclerosis patients. JCI Insight. 2(22):e92724 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA397295
    • Species: Homo Sapiens
    • IgRepSeq, mRNA
  24. Eliyahu, S. et al. Antibody Repertoire Analysis of Hepatitis C Virus Infections Identifies Immune Signatures Associated With Spontaneous Clearance. Front. Immunol. Dec. 21 (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJEB28370
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  25. Ellebedy, A.H. et al. Defining antigen-specific plasmablast and memory B cell subsets in blood following viral infection and vaccination of humans. Nat.
    Immunol. 17(10): 1226:1234 (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP075992
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  26. Fisher, C. et al. T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein. PLoS Pathog 13(7): e1006469 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA352758
    • Species: Mus Musculus
    • Illumina MiSeq, mRNA
  27. Fraussen, J. et al. Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD-CD27- Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients. J Immunol. 203(6): 1650-1664 (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA429427
    • Species: Homo sapiens
    • Illumina MiSeq
  28. Friedensohn, S. et al. Synthetic standards combined with errors and bias correction improve the accuracy and quantitative resolution of antibody repertoire sequencing in human naive and memory B cells. Front. Immunol. (2018). [DOI] [PubMed]
    • BioProject: PRJNA430091
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  29. Fu, L. et al. A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing. PLoS ONE 12(8): e0182733 (2017).
    [DOI]
    • Bioproject Accession: PRJNA389234
    • Species: Rhesus Macaque
    • Illumina HiSeq
  30. Gadala-Maria, D. et al. Identification of Subject-Specific Immunoglobulin Alleles from Expressed Repertoire Sequencing Data. Front Immunol. 10: 129 (2019).
    [DOI] [PubMed]
  31. Galson, J. et al. B-cell repertoire dynamics after sequential hepatitis B vaccination, and evidence for cross-reactive B-cell activation. Genome Medicine. 8(68):1-13 (2016)
    [DOI] [PubMed]
    • BioProject Accession: PRJNA308566
    • Species: Homo sapiens
    • Illumina MiSeq 2x300, mRNA
  32. Galson, J. et al. Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences. EBioMedicine. 2(12):2070-2079 (2015)
    [DOI] [PubMed]
    • BioProject Accession: PRJNA308641
    • Species: Homo sapiens
    • Illumina MiSeq 2x300, mRNA
  33. Galson, J. et al. BCR repertoire sequencing: different patterns of B cell activation after two Meningococcal vaccines. Immunology and Cell Biology. 93(10):885-95 (2015).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA335949
    • Species: Homo sapiens
    • Illumina MiSeq 2x250, mRNA
  34. Galson, J. et al. Investigating the effect of AS03 adjuvant on the plasma cell repertoire following pH1N1 influenza vaccination. Scientific Reports. 6:37229 (2016).
    [DOI] [PMC] [PubMed]
    • BioProject Accession: PRJNA336096
    • Species: Homo sapiens
    • Illumina MiSeq 2x300, mRNA
  35. Gidoni, M. et al. Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nature Communications, 10;628 (2019).
    [DOI]
    • SRA Accession: PRJEB26509
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  36. Greiff, V. et al. Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol. 15, 40 (2014).
    [DOI] [PubMed] [PMC]
    • ENA Accession: PRJEB4643
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x250, mRNA
  37. Greiff, V. et al. A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status. Genome Medicine, 7:49, (2015).
    [DOI] [PMC] [PubMed]
    • Data accession: Zenodo
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x250, mRNA
  38. Greiff, V. et al. Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development. Cell Reports, 19(17): 1467–1478 (2017).
    [DOI] [PubMed]
    • ENA accession: E-MTAB-5349
    • BioProject accession: PRJEB18631
    • Species: Mus musculus (C57BL/6, BALB/c, Pet store)
    • Illumina MiSeq 2x300, mRNA
    • Annotated sequences available at VDJServer
  39. Gupta, N.T. et al. Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data. J. Immunol. 1601850 (2017).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA349143
    • Illumina MiSeq 2x300, mRNA, 5’RACE, 17bp UMI
    • Annotated sequences available on VDJServer
  40. Halliley, J.L. et al. Long-Lived Plasma Cells Are Contained within the CD19(-)CD38(hi)CD138(+) Subset in Human Bone Marrow. Immunity 43:132-45 (2015).
    [DOI][PubMed] [PMC]
    • BioProject Accession: PRJNA280743
    • Species: Homo sapiens
    • Illumina MiSeq + HiSeq 1000, mRNA
  41. Hoehn, K.B. et al. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals. Philos. Trans. R. Soc. B Biol. Sci. 370, 20140241 (2015).
    [DOI] [PubMed] [PMC]
  42. Hong, B. et al. In-Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires. Front. Immunol. Feb 5 (2018).
    [DOI] [PubMed] [PMC]
  43. Jackson, K.J.L. et al. Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements. Cell Host Microbe, 105–114 (2014).
    [DOI] [PubMed] [PMC]
  44. Jiang, N. et al. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc. Natl. Acad. Sci. U. S. A. 108, 5348–53 (2011).
    [DOI]
  45. Jiang, N. et al. Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci. Transl. Med., 5, 171ra19 (2013).
    [DOI] [PubMed] [PMC]
  46. Joyce, M.G. et al. Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses. Cell. 166, 609-23 (2016).
    [DOI] [PubMed] [PMC]
    • BioProject Accession (Roche 454): PRJNA209999
    • BioProject Accession (Illumina MiSeq): PRJNA317685
    • Species: Homo sapiens
    • Roche 454, gDNA & mRNA; Illumina MiSeq 2x300 (?), mRNA, RACE
  47. Kaplinsky, J. et al. Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells. Proc. Natl. Acad. Sci. 111, E2622–E2629 (2014).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA248676
    • Species: Mus musculus
    • Illumina MiSeq 2x150, gDNA
  48. Khan, T. et al. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. Science Advances, 2, e1501371 (2016). [PubMed]
    • BioProject accession: PRJNA311999
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x300, mRNA
  49. Kleiman, E. et al. Epigenetic enhancer marks and transcriptIon factor binding influence V kappa gene rearrangement in pre-B cell and pro-B cells. Front. Immunol. Sept. 13 (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA483208
    • Species: Mus musculus
    • Illumina MiSeq
  50. Lehmann-Horn, K. et al. B cell repertoire expansion occurs in meningeal ectopic lymphoid tissue. JCI Insight.1(20):e87234 (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP078959
    • Species: Mus musculus
    • Ion torrent
  51. Levin, M. et al. Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy. J Allergy Clin Immunol, 137, 1535-1544 (2016) [DOI] [PubMed] [PMC]
    • BioProject accession: PRJNA391821
    • Species: Homo sapiens
    • Roche 454, mRNA
  52. Levin, M. et al. Antibody-encoding repertoires produced by cells of bone marrow and peripheral blood - a focus on IgE. J Allergy Clin Immunol, 139, 1026-1030 (2017) [DOI]
    • BioProject accession: PRJEB18926
    • Species: Homo sapiens
    • Illumina MiSeq 2x300, mRNA
  53. Li, X. et al. Comparative analysis of immune repertoires between bactrian camel’s conventional and heavy-chain antibodies. PLoS ONE 11(9): e0161801 (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA321369
    • Species: Camelus bactrianus
    • Illumina MiSeq, mRNA
  54. Liao, H.X. et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469 (2013).
    [DOI] [PMC]
  55. Lindner, C. et al. Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota. Nat. Immunol. 16, 880–888 (2015).
    [DOI] [PubMed]
    • ENA Accession: PRJEB9386
    • Species: Mus musculus
    • Roche 454, mRNA
  56. Lombardo, K.A. et al. High-throughput sequencing of the B-cell receptor in African Burkitt lymphoma reveals clues to pathogenesis. Blood Advances, 1:535 (2017).
    [DOI]
    • RNASeq and ImmunoSEQ, mRNA
    • SRA Accession: SRP099346
    • Adaptive Biotechnologies ImmuneACCESS
  57. Magadan, S. et al. Nasal Vaccination Drives Modifications of Nasal and Systemic Antibody Repertoires in Rainbow Trout. J Immunol. 203(6): 1480-1492 (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA551127
    • Species: Oncorhynchus mykiss
    • Illumina MiSeq
  58. Mattoo, H. et al. De novo oligoclonal expansions of circulating plasmablasts in active and relapsing IgG4-related disease. J. Allergy Clin. Immunol. 134(3):679-87 (2014).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  59. Meng, W. et al. An atlas of B-cell clonal distribution in the human body. Nat. Biotechnol. 35(9) (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA343738
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  60. Menzel, U. et al. Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing. PLoS One, e96727 (2014). [DOI] [PubMed] [PMC]
    • ENA Accession: PRJEB5238
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x250, mRNA
  61. Michaeli, M. et al. Immunoglobulin gene repertoire diversification and selection in the stomach - from gastritis to gastric lymphomas. Front. Immunol. 5, 1–14 (2014).
    [DOI] [PMC]
  62. Montague, Z. et al. Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity. MedXriv.
    • BioProject Accession: PRJNA645245
    • Illumina HiSeq 3000, RNA
    • Annotated sequences available on VDJServer
  63. Mroczek, E.S. et al. Differences in the Composition of the Human Antibody Repertoire by B Cell Subsets in the Blood. Front. Immunol. 5, 1–14 (2014).
    [DOI] [PubMed] [PMC]
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