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Publicly available AIRR-seq data sets: B cells (Continued)

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This page holds a continued list of B-cell papers for which there are publicly available AIRR-seq sequence data sets. By publicly available we mean data that is both available through an open data platform (such as the INSDC repositories - SRA/ENA) as well as data that is available as controlled data through a data sharing agreement with the research group and/or the data provider.

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 to the sources for those data sets are also available (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 papers or research groups that have such data sets, please add them to this list!

B Cell papers with data sets:

  1. Ohm-Laursen, L. et al. Local clonal diversification and dissemination of B lymphocytes in the human bronchial mucosa. Front. Immunol. Sept. 7 (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA422604
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  2. 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
  3. 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]
  4. Parameswaran, P. et al. Convergent Antibody Signatures in Human Dengue. Cell Host Microbe, 13, 691–700 (2013).
    [DOI] [PubMed] [PMC]
  5. 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
  6. 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
  7. Rettig, T. A. et al. Characterization of the naïve murine antibody repertoire using unamplified high-throughput sequencing. PLoS ONE 13(1): e0190982. (2018).
    [DOI] [PubMed] [PMC]
    • Genelab Accession: GLDS-141
    • Species: Mus musculus
    • Illumina MiSeq, mRNA
  8. Rosenfeld, A.M. et al. Computational Evaluation of B-cell clone sizes in bulk populations. Front. Immunol. Jun. 29 (2018).
    [DOI] [PMC]
    • SRA Accession: PRJNA476510
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  9. Roskin, K.M. et al. IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Sci. Transl. Med. 7, 302ra135 (2015).
    [PubMed] [PMC] [DOI]
    • dbGap Accession: phs000934.v1.p
    • ENA Accession: PRJNA287187
    • Species: Homo sapiens
    • Illumina MiSeq and Roche 454, mRNA and gDNA
  10. Roy, B. et al. High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease. J. Immunol. 199 (2) (2017).
    [DOI] [PubMed]
  11. Rubelt, F. et al. Individual heritable differences result in unique Lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat. Commun. 7, 1–12 (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP065626
    • ImmPort Accession (processed data): SDY675
    • Illumina MiSeq 2x300, mRNA, 5’RACE, 10bp UMI
    • Annotated sequences available at VDJServer
  12. Schanz, M. et al. High-Throughput Sequencing of Human Immunoglobulin Variable Regions with Subtype Identification. PLoS ONE 9(11): e111726 (2014).
    [DOI] [PubMed] [PMC]
  13. Seay, H.R. et al. Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes. JCI Insight, 1(20):e88242 (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
    • Annotated sequences available on iReceptor
  14. Silver, J. et al. Stochasticity enables BCR-independent germinal center initiation and antibody affinity maturation. JEM 20171022 (2017) [DOI]
    • Bioproject Accession: PRJNA388102
    • Species: Mus Musculus
    • Illumina MiSeq mRNA
  15. Snir, O. et al. Stereotyped antibody responses target posttranslationally gluten in celiac disease. JCI insight 2(17): e93961. (2017). [DOI] [PMC]
    • Bioproject Accession: SRP098633
    • Illumina MiSeq, mRNA
    • Annotated sequences available on iReceptor
  16. Sok, D. et al. The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog 9(11): e1003754 (2013).
    [DOI] [PubMed] [PMC]
    • CDR3 in paper and raw sequences: s3://hiv-antibody-data
    • Roche 454, mRNA
  17. Soto, C. et al. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. PLoS One. 11(6):e0157409 (2016).
    [DOI] [PMC] [PubMed]
  18. Soto, C. et al. High frequency of shared clonotypes in human B cell receptor repertoires. Nature, 566, 398-402 (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA511481
    • Species: Homo Sapiens
    • Illumina MiSeq, mRNA
    • Annotated sequences available at VDJServer
  19. Stern, J.N.H. et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci. Transl. Med. 6, 248ra107 (2014).
    [DOI] [PubMed] [PMC]
  20. Su, K.Y. et al. Efficient Culture of Human Naïve and Memory B cells for use as antigen-presenting cells. J. Immunol. 197(10):4163-4176 (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  21. Sundling, C. et al. Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization. J. Immunol. 192, 3637–3644 (2014).
    [DOI] [PubMed] [PMC]
  22. Tian, M. et al. Induction of HIV Neutralizing Antibody Lineages in Mice with Diverse Precursor Repertoires. Cell. 166(6): 1471-1484 (2016).
    [DOI][PubMed]
    • BioProject Accesion: PRJNA327421
    • Species: Mus musculus
    • Illumina MiSeq 2x250, single cell emulsion PCR-linked heavy and light chain
  23. Tipton, C.M. et al. Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosus. Nat. Immunol. (2015).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP057017
    • Illumina MiSeq 2x250/2x300, mRNA
    • Annotated sequences available on iReceptor
  24. Tong, P. et al. IGH isotype-specific B cell receptor expression influences B cell fate. PNAS 114(40):E8411-E8420 (2017).
    [DOI] [PubMed] [PMC]
    • Bioproject Accession: PRJNA394007
    • Adaptive Biotech
    • Species: Mus Musculus
    • Illumina MiSeq, mRNA
  25. Tsioris, K. et al. Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing. Integr. Biol. 7, 1587–1597 (2015).
    [DOI] [PMC]
  26. Turchaninova, M. et al. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nature Protocols 11, 1599–1616 (2016).
    [DOI][PubMed]
    • BioProject Accession: PRJNA297771
    • Species: Homo sapiens
    • Illumina MiSeq 350+300/400+100, mRNA, 5’RACE, 12bp UMI
  27. Valdés-Alemán, J. 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: PRJNA275625
    • Species: Homo Sapiens
    • Illumina MiSeq, mRNA
    • Annotated sequences available on iReceptor
  28. Vander Heiden, J.A. et al. Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing. J. Immunol. 1601415 (2017).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA338795
    • Illumina MiSeq 2x300, mRNA, 5’RACE, 17bp UMI
  29. VanDuijn, M.M. et al. Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. Front Immunol. 8: 1286 (2017).
    [DOI][PMC]
    • Bioproject Accession: PRJNA386462
    • Species: Rattus norvegicus
    • Illumina MiSeq, mRNA
  30. Vergani, S. et al. Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution. Front Immunol. 8: 1157 (2017).
    [DOI] [PMC]
  31. Vollmers, C. et al. Genetic measurement of memory B-cell recall using antibody repertoire sequencing. Proc. Natl. Acad. Sci. U. S. A., 110, 13463–8 (2013).
    [DOI] [PMC]
  32. Vollmers, C. et al. Novel Exons and Splice Variants in the Human Antibody Heavy Chain Identified by Single Cell and Single Molecule Sequencing. PLoS One 10, e0117050 (2015).
    [DOI] [PMC]
    • SRA Accession: SRP043513
    • Illumina HiSeq2000, mRNA, PacBio, Sanger
  33. Wang, C. et al. Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. J. Immunol., 192, 603–11 (2014).
    [DOI] [PMC]
  34. Wang, C. et al. B-cell repertoire responses to varicella-zoster vaccination in human identical twins. Proc. Natl. Acad. Sci. U. S. A. (2014).
    [DOI] [PMC]
  35. Weinstein, J.A. et al. High-throughput sequencing of the zebrafish antibody repertoire. Science (80-. ). 324, 807–10 (2009).
    [DOI] [PMC]
  36. Wesemann, D.R. et al. Microbial colonization influences early B-lineage development in the gut lamina propria. Nature 501, 112–5 (2013).
    [DOI]
  37. Wu, X. et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science (80-. ). 333, 1593–602 (2011).
    [DOI] [PMC]
  38. Wu, X. et al. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell. 161(3):470-85 (2015).
    [DOI] [PMC]
    • SRA Accession: SRP052625
    • Roche 454, mRNA, VH1/VK-specific multiplex PCR
    • Annotated sequences available on VDJServer
  39. Wu, Y.C. et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J. Allergy Clin. Immunol. 134, 604–612 (2014).
    [DOI] [PMC]
  40. Yang, Y. et al. Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires. eLife 4: e09083 (2015).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP078465
    • Species: Mus musculus
    • Illumina MiSeq, mRNA
  41. Zhang, C. et al. Impact of a 3-Months Vegetarian Diet on the Gut Microbiota and Immune Repertoire. Front. Immunol. 9:908 (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: ERP108062
    • Species: Homo sapiens
    • Illumina HiSeq 2000
  42. Zhang, W. et al. Identification of Variable and Joining Germline Genes and Alleles for Rhesus Macaque from B Cell Receptor Repertoires. J. Immunol. 202(5) (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA503527
    • Species: Macaca mulatta
    • Illumina MiSeq
  43. Zhou, T. et al. Multi-donor Analysis Reveal Structural Elements, Genetic Determinants, and Maturation Pathway for Effective HIV-1 Neutralization by VRC01-class Antibodies. Immunity. 39, 245-258 (2013).
    [DOI] [PMC]
  44. Zhou, T. et al. Structural repertoire of HIV-1 neutralizing antibodies targeting the CD4 supersite in 14 donors. Cell, 6 1280-1292 (2015).
    [DOI]
  45. Zhu, J. et al. Somatic Populations of PGT135-137 HIV-1-Neutralizing Antibodies Identified by 454 Pyrosequencing and Bioinformatics. Frontiers in Microbiology. 3, 315 (2012).
    [DOI] [PMC]
  46. Zhu, J. et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc. Natl. Acad. Sci. U. S. A. 110, 6470–5 (2013).
    [DOI] [PMC]
  47. Zhu, J. et al. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. PNAS. 110, 4088-4097 (2013).
    [DOI] [PMC]
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Publicly available AIRR-seq data sets: B cells
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