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. 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
  7. 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
  8. 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
  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(2017).
    [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
  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, 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
  17. 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
  18. 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
  19. 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.
  20. 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]
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. Hong, B. et al. In-Depth Analysis of Human Neonatal and Adult IgM Antibody Repertoires. Front. Immunol. Feb 5 (2018).
    [DOI] [PubMed] [PMC]
  37. 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
  38. 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]
  39. 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]
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. Liao, H.X. et al. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature 496, 469 (2013).
    [DOI] [PMC]
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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]
  52. 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]
  53. 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
  54. 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]
  55. Parameswaran, P. et al. Convergent Antibody Signatures in Human Dengue. Cell Host Microbe, 13, 691–700 (2013).
    [DOI] [PubMed] [PMC]
  56. 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
  57. 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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