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


#1
  1. 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
  2. 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.p1
    • Species: Homo sapiens
    • Illumina MiSeq and Roche 454, mRNA and gDNA
  3. Rubelt, F. et al. Individual heritable differences result in unique Lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat. Commun. 6, 1–12 (2016).
    [DOI] [PubMed] [PMC]

    • SRA Accession: SRP065626
    • ImmPort Accession (processed data): SDY675
    • Illumina MiSeq 2x300, mRNA, 5’RACE, 10bp UMI
  4. Schanz, M. et al. High-Throughput Sequencing of Human Immunoglobulin Variable Regions with Subtype Identification. PLoS ONE 9(11): e111726 (2014).
    [DOI] [PubMed] [PMC]

  5. Silver, J. et al. Stochasticity enables BCR-independent germinal center initiation and antibody affinity maturation. JEM 20171022 (2017) [DOI]

    • Bioproject Accession: SRP057017
    • Species: Homo Sapiens
    • Illumina MiSeq mRNA
  6. 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
  7. 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
  8. Soto, C et al. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. PLoS One. 11(6):e0157409 (2016).
    [DOI] [PMC] [PubMed]

  9. 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]

    • BioProject Accession: PRJNA248475
    • Illumina MiSeq 2x250, mRNA, 17bp UMI
    • Annotated sequences available on iReceptor
  10. 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]

  11. 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
  12. 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
  13. 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
  14. 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]

    • dbGap Accession: phs001200.v1.p1
    • Illumina MiSeq 2x150/2x300, mRNA, 5’RACE, 12/15bp UMI
  15. 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
  16. 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
  17. VanDuijn, M. M. et al. Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. Front Immunol. 8: 1286 (2018).
    [DOI][PMC]

    • Bioproject Accession: PRJNA386462
    • Species: Rattus norvegicus
    • Illumina MiSeq, mRNA
  18. 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]

  19. 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]

    • dbGAP Accession: phs000656.v1.p1
    • Illumina HiSeq2000 100+120, mRNA, 2x8bp UMI
  20. 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
  21. 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]

    • dbGAP Accession: phs000666.v1.p1
    • Roche 454, gDNA/mRNA
  22. 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]

    • dbGAP Accession: phs000817.v1.p1
    • Roche 454, gDNA/mRNA
  23. Weinstein, J. A. et al. High-throughput sequencing of the zebrafish antibody repertoire. Science (80-. ). 324, 807–10 (2009).
    [DOI] [PMC]

  24. Wesemann, D. R. et al. Microbial colonization influences early B-lineage development in the gut lamina propria. Nature 501, 112–5 (2013).
    [DOI]

  25. 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]

  26. 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
  27. Wu, Y.-C. B. 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]

  28. 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: SRA440320
    • Species: Mus musculus
    • Illumina MiSeq, mRNA
  29. 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]

  30. Zhou, T. et al. Structural repertoire of HIV-1 neutralizing antibodies targeting the CD4 supersite in 14 donors. Cell, 6 1280-1292 (2015).
    [DOI]

  31. 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]

  32. 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]

  33. 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]


B-T.CR Wiki Home