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Publicly available AIRR-seq data sets: T Cells (Continued)

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This page holds a list of T-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!

T Cell papers with data sets:

  1. Oakes, T. et al. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front. Immunol. 8:1267 (2017).
    [DOI][PubMed]
  2. Ostmeyer, J. et al. Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma. PLoS One. Mar 5;15(3):e0229569 (2020).
    [DOI] [PubMed] [PMC]
    • Species: Homo sapiens
    • ImmunoSEQ, DNA
    • Annotated sequences available at VDJServer
  3. Ott de Bruin, L.M. et al. Hypomorphic Rag1 mutations alter the pre-immune repertoire at early stages of lymphoid development. Blood, 132(3):281-292 (2018).
    [DOI] [PubMed]
    • Species: Mus musculus
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  4. Page, D.B. et al. Deep sequencing of T-cell receptor DNA as a biomarker of clonally expanded TILs in breast cancer after immunotherapy. Cancer Immunol. Res. 4, 835 (2016).
    [DOI] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  5. Palomero, T. et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat Genet. 46(2):166-70 (2014). [DOI] [PubMed] [PMC]
  6. Patas, K. et al. T Cell Phenotype and T Cell Receptor Repertoire in Patients with Major Depressive Disorder. Front Immunol. 9:291 (2018).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
  7. Peterson, V.M. et al. Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol. 35(10):936-939 (2017).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA391958
    • Species: Homo Sapiens
    • Illumina HiSeq, mRNA
  8. Pogorelyy, M.V. et al. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. PLoS Comput Biol. 13(7):e1005572 (2017).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA329041
    • SRA Accession: SRP078490
    • Species: Homo sapiens
    • Illumina HiSeq 2000
  9. Pogorelyy, M.V. et al. Precise tracking of vaccine-responding T cell clones reveals convergent and personalized response in identical twins. Proc. Natl. Acad. Sci. USA 115(50) (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA493983
    • Species: Homo sapiens
    • Illumina HiSeq 2500, mRNA
    • Annotated sequences available on iReceptor
  10. Putintseva, E. V et al. Mother and child T cell receptor repertoires: deep profiling study. Front. Immunol. 4, 463 (2013).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA229070
    • Illumina HiSeq 2000 2x100, mRNA
    • Annotated sequences available on iReceptor
  11. Qi, Q. et al. Diversity and clonal selection in the human T-cell repertoire. Proc. Natl. Acad. Sci. U. S. A (2014).
    [DOI] [PubMed] [PMC]
  12. Ramien, C. et al. T Cell Repertoire Dynamics during Pregnancy in Multiple Sclerosis. Cell Reports 29(4):810-815.e4 (2019).
    [DOI] [PMC]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies
  13. Robert, L. et al. CTLA4 Blockade Broadens the Peripheral T-cell receptor repertoire. Clin. Cancer Res. 20(9): 2424 (2014).
    [DOI] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  14. Rossetti, M. et al. TCR Repertoire sequencing identifies synovial Treg cell clonotypes in the bloodstream during active inflammation in human arthritis. Ann. Rheum. Dis. 208992 (2016).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  15. Rowe, J.H. et al. Abnormalities of T-cell receptor repertoire in CD4+ regulatory and conventional T cells in patients with RAG mutations: Implications for autoimmunity. J. Allergy Clin Immunol. 140(6):1739-1743 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  16. 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
    • Annotated sequences available at VDJServer
  17. Rudqvist, N.P. et al. Radiotherapy and CTLA-4 blockade shape the TCR repertoire of tumor-infiltrating T cells. Cancer Immunol. Res. 6(2):139-150 (2018).
    [DOI] [PubMed]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  18. Ruggiero, E. et al. High-resolution analysis of the human T-cell receptor repertoire. Nature Communications 6, 8081 (2015).
    [DOI] [PubMed] [PMC]
  19. Saligrama, N. et al. Opposing T cell responses in experimental autoimmune encephalomyelitis. Nature 572(7770): 481-487 (2019).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA542157
    • Geo Accession: GSE130975
    • Species: Mus musculus
    • Illumina HiSeq 4000
  20. Savola, P. et al. Somatic mutations in clonally expanded cytotoxic T lymphocytes in patients with newly diagnosed rheumatoid arthritis. Nat. Commun. 8:15869 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  21. 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
  22. Sherwood, A.M. et al. Tumour-infiltrating lymphocytes in colorectal tumors display a diversity of T cell receptor sequences that differ from the T cells in adjacent mucosal tissue. Cancer Immunol. Immunother. 9, 1453 (2013).
    [DOI]
    • CDR3 in paper
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  23. Shi, L. et al. Multi-omics study revealing the complexity and spatial heterogeneity of tumor-infiltrating lymphocytes in primary liver carcinoma. Oncotarget, 8(21):34844-34857 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP094909
    • Species: Homo Sapiens
    • Illumina HiSeq 2500, mRNA
    • Annotated sequences available on iReceptor
  24. Shugay, M. et al. Towards error-free profiling of immune repertoires. Nature, 11(6) (2014).
    [DOI] [PubMed]
    • SRA Accession: PRJNA239303
    • Species: Homo sapiens
    • Illumina HiSeq 2500, mRNA
  25. Shugay, M. et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11, 1–16 (2015).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA280417
    • Illumina HiSeq2500, mRNA, 5’RACE, 12bp UMI
  26. Simoni, Y. et al. Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates. Nature 557(7706):575-579 (2018).
    [DOI] [PubMed]
  27. Sims, J.S. et al. Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. proc. Natl. Acad. Sci. USA 113(25) (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA315543
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  28. Simnica, D. et al. High-throughput immunogenetics reveals a lack of physiological t cell clusters in patients with autoimmune cytopenias. Front Immunol. 10:1897 (2019).
    [DOI] [PubMed] [PMC]
    • Bioproject Accession: PRJEB33806
    • Species: Homo sapiens
    • Illumina MiSeq
  29. Song, J. et al. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope. Nat. Struct. Mol. Biol. 24(4):395-406 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  30. Spreafico, R. et al. A circulating reservoir of pathogenic-like CD4+ T cells shares a genetic with the inflamed synovial micro-environment. Annals of Rheumatic Diseases, Vol. 75, Iss. 2 (2015).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  31. Stromnes, I.M. et al. T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma. Cancer Immunol. Research Vol. 5 Issue 11 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq, mRNA
    • Adaptive Biotechnologies
  32. Tanno, H. et al. Determinants Governing T Cell Receptor α/β-chain Pairing in Repertoire Formation of Identical Twins. PNAS 2020 Jan 7;117(1):532-540.
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA593622
    • Bulk paired-chain, mRNA
    • Annotated sequences available at VDJServer
  33. Textor, J. et al. Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response. J Immunol. 201(2):350-358 (2018).
    [DOI] [PubMed]
    • Illumina MiSeq, mRNA
    • SRA Accession: PRJNA776826
    • Annotated sequences available on GitHub
  34. Theil, A. et al. T cell receptor repertoires after adoptive transfer of expanded allogeneic regulatory T cells. Clin Exp Immunol. 187(2):316-324 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq, mRNA
    • Species: HomoSapiens
    • Annotated sequences available at VDJServer
  35. Tran, E. et al. Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science 344, 641 (2014).
    [DOI] [PubMed]
    • SRA Accession: PRJNA243084
    • ImmunoSEQ (Adaptive Biotechnologies), mRNA
  36. Tumeh, P.C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature, 515, 568 (2014).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  37. Wallin, J.J. et al. Atezolizumab in combination with bevacizumab enhances migration of antigen-specific T-cells in metastatic renal cell carcinoma. Nat. Commun. 7, 12624 (2016).
    [DOI] [PMC]
  38. Wang, C. et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets. Proc. Natl. Acad. Sci. U.S.A. 107, 1518–23 (2010).
    [DOI] [PMC]
  39. Wang, T. et al. The different T-cell receptor repertoires in breast cancer tumors, draining lymph nodes, and adjacent tissues. Cancer Immunol Res., 5(2): 148-156 (2017).
    [DOI] [PubMed]
    • SRA Accession: SRA455606
    • Illumina HiSeq 2000, mRNA
    • Annotated sequences available on iReceptor
  40. Warren, R.L. et al. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes. Genome Res., 21, 790–7 (2011).
    [DOI] [PMC]
    • SRA Accession: SRA020989
    • Illumina GA IIx 2x100/2x150, mRNA, 5’RACE
  41. Wendel, B.S. et al. A Streamlined Approach to Antibody Novel Germline Allele Prediction and Validation. Front. Immunol. 8:1072 (2017).
    [DOI] [PubMed] [PMC]
  42. Wu, D. et al. High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia. Sci. Transl. Med. 4(134):134ra63 (2012).
    [DOI] [PubMed]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  43. Yan, T. et al. Multi-region sequencing unveils novel actionable targets and spatial heterogeneity in esophageal squamous cell carcinoma. Nat. Commun. 10(1):1670 (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA511368
    • Species: Homo sapiens
    • Illumina HiSeq X-Ten, mRNA
  44. Yang, G. et al. Next generation sequencing of the Pig alpha-beta TCR Repertoire Identifies the porcine invariant NKT Cell Receptor. J. Immunol. 202(7):1981-1991 (2019).
    [DOI] [PubMed]
    • SRA Accession: SRP156281
    • Species: Sus scrofa
    • Illumina NextSeq 500, mRNA
  45. 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
  46. Zvyagin, I.V. et al. Distinctive properties of identical twins’ TCR repertoires revealed by high-throughput sequencing. Proc. Natl. Acad. Sci. U. S. A. 111, 5980–5 (2014).
    [DOI] [PMC]
    • SRA Accession: SRP028752
    • Species: HomoSapiens
    • Illumina GA IIx 2x125, mRNA
  47. Zvyagin, I.V. et al. Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children. Leukemia. 5, 1145-53 (2017).
    [DOI] [PubMed]
    • SRA Accession: SRP070495
    • BioProject Accession: PRJNA312319
    • Species: HomoSapiens
    • Illumina HiSeq2500 2x100, mRNA, 5’RACE, UMI
    • Annotated sequences available on iReceptor
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Publicly available AIRR-seq data sets: B cells
Publicly available AIRR-seq data sets: B cells (Continued)