Publicly available AIRR-seq data sets: T cells


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  1. Bobisse, S. et al. Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naïve ovarian cancer. Nat. Commun. 9: 1092 (2018).
    [DOI] [PubMed] [PMC]
    • EGA Accession: EGAS00001002803
    • Species: Homo Sapiens
    • Illumina HiSeq, mRNA
  2. Britanova, O. V et al. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. J. Immunol. 192, 2689–98 (2014).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA273698
    • Illumina HiSeq2000 2x100, mRNA, 5’RACE, UMI
  3. Britanova, O. V. et al. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. J. Immunol. (2016).
    [DOI] [PubMed]
    • BioProject Accession: PRJNA316572
    • Illumina HiSeq2500 2x100, mRNA, 5’RACE, UMI
    • Data from Britanova et al. 2014 is a subset of this dataset
  4. Chen, Z. et al. T cell receptor b-chain repertoire analysis reveals intratumour heterogeneity of tumour-infiltrating lymphocytes in oesophageal squamous cell carcinoma. J. Pathol. 4, 450 (2016).
    [DOI] [PubMed]
    • SRA Accession: SRP072206
    • Illumina HiSeq 2000, mRNA
  5. Davey, M.S. et al. Clonal selection in the human Vdelta1 Tcell repertoire indicates gd-TCR dependent adaptive immune surveillance. Nature Comm. 8, 14760 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP096009
    • Illumina MiSeq, cDNA
  6. Feng, L et al. Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme. Scientific Reports, 7, 6968 (2017).
    [DOI]
  7. Feng, Y. et al. A mechanism for expansion of regulatory T-cell repertoire and its role in self-tolerance. Nature 528, 132–136 (2015).
    [DOI] [PubMed] [PMC]
  8. Freeman, J.D. et al. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res., 19, 1817–24 (2009).
    [DOI][PubMed] [PMC]
    • SRA Accession: SRA008633
    • Illumina GA II, mRNA, 5’RACE
  9. 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] [PubMed] [PMC]
    • Bioproject Accession: PRJNA389234
    • Species: Rhesus Macaque
    • Illumina HiSeq
  10. Gee, M.H. et al. Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes. Cell 11.043 (2017).
    [DOI] [PubMed]
    • SRA Accession: PRJNA417113
    • Yeast display library
    • Illumina MiSeq, mRNA
  11. Heather, J.M. et al. Dynamic Perturbations of the T-Cell Receptor Repertoire in Chronic HIV Infection and following Antiretroviral Therapy. Front. Immunol. 6:644 (2016).
    [DOI][PubMed]
    • BioProject Accession: PRJNA258001
    • Species: Homo sapiens
    • Illumina MiSeq, 250 bp, mRNA 5’ RACE, 12 bp UMI
  12. Huang, J et al. Identification of a CD4-Binding-Site Antibody to HIV that Evolved Near-Pan Neutralization Breadth. Immunity. 45(5):1108-1121 (2016).
    [DOI] [PubMed] [PMC]
    • BioProject Accession: PRJNA347514
    • Illumina MiSeq 2x300, mRNA, 5’RACE
  13. Kallemaijn, M.J. et al. Next-generation sequencing analysis of the human TCR gamma delta+ T-cell repertoire reveals differential Vgamma and Vdelta-usage in memory populations upon aging. Front. Immunol. 06 March 2018.
    [DOI]
    • Bioproject Accession: PRJNA434217
    • Species: Homo Sapiens
    • Illumina TruSeq, mRNA
  14. Komech, E. A. et al. CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Rheumatology (Oxford). [Epub ahead of print] (2018).
    [DOI] [PubMed]
    • SRA Accession: SRP111372
    • BioProject Accession: PRJNA393498
    • Species: HomoSapiens
    • Illumina HiSeq2500 2x100, mRNA, 5’RACE, UMI
  15. Kuang, M. et al. A novel signature for stratifying the molecular heterogeneity of the tissue-infiltrating T-cell receptor repertoire reflects gastric cancer prognosis. Sci Rep, 7; 7762 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP091344
    • Species: Homo Sapiens
    • Illumina HiSeq, mRNA
  16. Ma, K.Y. et al. Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification. Front. Immunol. Feb. 5 (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP128082
    • Species: Homo sapiens
    • Illumina NextSeq 500, mRNA
  17. Maceiras, A. R. et al. T follicular helper and T follicular regulatory cells have different TCR specificity. Nat Commun. 8:15067 (2017)
    [DOI][PubMed]
    • BioProject Accession: PRJNA362309
    • Species: Mus musculus
    • Illumia MiSeq 2x250, mRNA
  18. Madi, A. et al. T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res. 24, 1603–1612 (2014).
    [DOI] [PubMed] [PMC]
    • SRA Accession: SRP042610
    • Illumina HiSeq 2000, mRNA
  19. Madi, A. et al. T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences. eLife 6: e22057 (2017).
    [DOI] [PubMed] [PMC]
    • Files: Galaxy
    • Species: Mus Musculus
    • Illumina, Adaptive Biotechnologies, mRNA
  20. Mamedov, I.Z. et al. Quantitative tracking of T cell clones after hematopoietic stem cell transplantation. EMBO Mol. Med. 3, 201-207 (2011).
    [DOI] [PMC] [PubMed]
  21. Martin, S.D. et al. Low mutation burden in ovarian cancer may limit the utility of neoantigen-targets vaccines. PLoS One, e0155189 (2016)
    [DOI]
    • SRA Accession: SRP069102
    • Illumina HiSeq 2000, mRNA
  22. Munson, D.J. et al. Identification of shared TCR sequences from T cells in human breast cancer using emulson RT-PCR. Proc. Natl. Acad. Sci USA 113(29): 8272–8277 (2016).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA321261
    • Species: Homo Sapiens
    • Illumina MiSeq, mRNA
  23. 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]
  24. 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
  25. 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]
  26. 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
  27. Ruggiero, E. et al. High-resolution analysis of the human T-cell receptor repertoire. Nature Communications 6, 8081 (2015).
    [DOI] [PubMed] [PMC]
  28. 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
  29. 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
  30. 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
  31. 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]
  32. Wang, T. et al. The different T-cell receptor repertoirs in breast cancer tumors, draining lymph nodes, and adjacent tissues. AACR (2016).
    [DOI] [PubMed]
    • SRA Accession: SRA455606
    • Illumina HiSeq 2000, mRNA
  33. 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
  34. Wendel, B. S. et al. A Streamlined Approach to Antibody Novel Germline Allele Prediction and Validation. Front. Immunol. 8:1072 (2017).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA342513
    • Species: Homo Sapiens
    • Illumina MiSeq, mRNA
  35. 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
  36. 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