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
    • Annotated sequences available on iReceptor
  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 cannot locate this data.
    • Annotated sequences available on iReceptor
  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
    • Annotated sequences available on iReceptor
  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
    • Annotated sequences available on iReceptor
  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
    • Annotated sequences available on iReceptor
  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
    • Annotated sequences available on iReceptor
  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. 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]

    • BioProject: PRJNA430091
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. Hong, B. et al. In-Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires. Front. Immunol. Feb 5 (2018).
    [DOI] [PubMed] [PMC]

  35. 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
  36. 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]

  37. 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]

  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. Liao, H.X. et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469 (2013).
    [DOI] [PMC]

  45. 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
  46. 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
  47. 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]

  48. 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]

  49. 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
  50. 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]

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

  52. 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
  53. 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

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