Publicly available AIRR-seq data sets: B cells


#1
  1. Aleman, JV, Barnetche JM et al. Hybridization-based antibody cDNA recovery for the production of recombinant antibodies identified by repertoire sequencing. Landes Bioscience V 6:1, 493-501 (2014).
    [DOI] [PubMed][PMC]

    • BioProject Accession: PRJNA248475
    • Species: Homo Sapiens
    • Illumina MiSeq, mRNA
  2. 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
  3. Bashford-Rogers, RJ 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
    • Species: Homo sapiens
    • Roche 454, mRNA
    • The publication also states Illumina MiSeq 2x250, but I cannot locate this data.
  4. 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]

  5. Bolland, DJ 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
  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]

    • BioProject Accession: PRJNA304166
    • Species: Homo sapiens
    • Roche 454, gDNA
  7. Boyd, SD 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
  8. 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
  9. Chen, Y. et al. Microbial symbionts regulate the primary Ig repertoire. Jem 1761(2017).
    [DOI] [PubMed]

  10. 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
  11. 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
  12. 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: Macaca mulatta, Mus musculus
    • MiSeq 2x300bp, mRNA
  13. 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
  14. 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]

  15. DeKosky, BJ 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
  16. DeKosky, BJ 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
  17. 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.
  18. 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]

  19. 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
  20. 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
  21. 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
  22. 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.
    [DOI]

    • Bioproject Accession: PRJNA389234
    • Species: Rhesus Macaque
    • Illumina HiSeq
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Greiff, V. et al. Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development. Cell Reports, 19, 1467–1478 (2015).
    [DOI] [PubMed]

    • ENA accession: E-MTAB-5349
    • Species: Mus musculus (C57BL/6, BALB/c, Pet store)
    • Illumina MiSeq 2x300, mRNA
  30. 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
  31. Halliley, JL 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
  32. 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]

    • ENA Accession: ERP000572
    • Illumina MiSeq 2x150, mRNA
  33. Hong, B. et al. In-Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires. Front. Immunol. Feb 5 (2018).
    [DOI] [PubMed] [PMC]

  34. 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]

    • dbGaP Accession: phs000760.v1.p1
    • Roche 454, gDNA
  35. 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]

  36. 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]

  37. 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
  38. 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
  39. Khan, T. et al. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. Science Advances, 2, e1501371 (2016). [DOI]

    • BioProject accession: PRJNA311999
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x300, mRNA
  40. 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
  41. Levin, M. et al. Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy. J Allergy Clin Immunol, 137, 1535-1544 (2015) [DOI] [PubMed] [PMC]

    • BioProject accession: PRJNA391821
    • Species: Homo sapiens
    • Roche 454, mRNA
  42. 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
  43. Liao, H.X. et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469 (2013).
    [DOI] [PMC]

  44. 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
  45. 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: E-MTAB-2226
    • Species: Mus musculus (BALB/c)
    • Illumina MiSeq 2x250, mRNA
  46. 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]

  47. 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]

  48. Ota, M. et al. Regulation of the B Cell Receptor Repertoire and Self-Reactivity by BAFF. J. Immunol. 185, 4128–4136 (2010).
    [DOI] [PubMed] [PMC]

    • BioProject Accession: PRJNA79689
    • Species: Mus musculus
    • Roche 454, mRNA, 5’RACE
  49. Palanichamy, A. et al. Immunoglobulin class-switched B cells form an active immune axis between CNS and periphery in multiple sclerosis. Sci. Transl. Med. 6, 248ra106–248ra106 (2014).
    [DOI] [PubMed] [PMC]

  50. Parameswaran, P. et al. Convergent Antibody Signatures in Human Dengue. Cell Host Microbe, 13, 691–700 (2013).
    [DOI] [PubMed] [PMC]

  51. Pieper, K. et al. Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature, Letter, August 23, 2017.
    [DOI] [PubMed] [PMC]

    • BioProject Accession: PRJNA382214
    • Illumina MiSeq, mRNA
  52. Prohaska, T.A. et al. Massively parallel sequencing of peritoneal and splenic B cell repertoires highlights unique propertied of B-1 cell antibodies. J. Immunol. 200(5):1702-1717. (2018).
    [DOI] [Pubmed]

    • Bioproject Accession: PRJNA418221
    • Species: Mus Musculus
    • Illumina MiSeq 2x300bp, mRNA