Publicly available AIRR-seq data sets: T cells


#1
  1. Abdel-Hakeem, M.S. et al. Selective expansion of high functional avidity memory CD8 T cell clonotypes during hepatitis C virus reinfection and clearance. PLoS Pathog. 13(2):e1006191 (2017).
    [DOI] [PubMed] [PMC]
    • Illumina, mRNA
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
  2. Allenspach, E.J. et al. Absence of functional fetal regulatory T cells in humans causes in utero organ-specific autoimmunity. J. Allergy Clin. Immunology, 140(2):616-619.e7 (2017).
    [DOI] [PubMed]
    • Illumina, mRNA
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
  3. Arrieta- Bolanos, E. et al. Alloreactive T cell receptor diversity against structurally similar or dissimilar HLA-DP Antigens Assessed by Deep Sequencing. Front. Immunol. 9:280 (2018).
    [DOI] [PubMed] [PMC]
    • TCR Immunosequencing
    • ImmunoSEQ Analyzer
    • Adaptive Biotechnologies ImmuneACCESS
  4. Beausang, J.F. et al. T cell receptor sequencing of early-stage breast cancer tumors identifies altered clonal structure of the T cell repertoire. Proc Natl Acad Sci USA, 114(48): E10409–E10417 (2017).
    [DOI] [PUbMed] [PMC]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies ImmuneACCESS
  5. Beccatini, S. et al. Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines. Science, 347(6220):400-6 (2015).
    [DOI] [PubMed]
    • ImmunoSEQ, gDNA
    • Adaptive Biotechnologies ImmuneACCESS
  6. Blank, C. et al. Neoajuvant versus adjuvant ipilimumab plus nivolumab in macroscopic stage III mela. Nat. Med. 24(11) (2018).
    [DOI] [PubMed]
    • EGA Accession: EGAD00001004217
    • Species: Homo sapiens
    • Illumina HiSeq 2500, mRNA
  7. 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
  8. 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
  9. 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
  10. Carey, A.J. et al. Rapid evolution of the CD8+ T cell receptor repertoire in neonatal mice. J. Immunol. 196(6):2602-13 (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, cDNA
    • Adaptive Biotechnologies ImmuneACCESS
  11. Carey, A.J. _et al._Public clonotypes and Convergent Recombination Characterize the Naïve CD8+ T-cell Receptor Repertoire of Extremely Preterm Neonates. Front. Immunol. 8:1859 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, cDNA
    • Adaptive Biotechnologies ImmuneACCESS
  12. 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
    • Annotated sequences available on iReceptor
  13. Cheuk, S. _et al._CD49a Expression Defines Tissue-Resident CD8+ T cells Poised for Cytotoxic Function in Human Skin. Immunity, 46(2):287-300 (2017).
    [DOI] [PubMed] [PMC]
    • Species: Homo sapiens
    • Adaptive Biotechnologies ImmuneACCESS
  14. Clave, E. et al. Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus. Sci Transl Med. 10:457 (2019).
    [DOI] [PubMed]
    • Species: Homo sapiens
    • Adaptive Biotechnologies ImmuneACCESS
  15. 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
  16. Dean, J. et al. Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci. Genome Medicine 7, 123 (2015).
    [DOI]
  17. DeWitt, W.S. et. al. Dynamics of the cytotoxic T cell response to a model of acute viral infection. J. Virol. 89(8):4517-26 (2015).
    [DOI] [PubMed] [PMC]
    • Illumina, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  18. Emerson, R. et al. Estimating the ratio of CD4+ to CD8+ T cells using high-throughput sequence data. J. Immunol. Methods, 391(1-2):14-21 (2013).
    [DOI] [PubMed]
    • Illumina HiSeq, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  19. 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]
    • SRA Accession: PRJNA325416
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
    • Annotated sequences available on iReceptor
  20. 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]
  21. 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
  22. 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
  23. Gaide, O. et al. Common clonal origin of central and resident memory T cells following skin immunization. Nat. Med. 21(6):647-53 (2015).
    [DOI] [PubMed] [PMC]
    • Illumina HiSeq, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  24. 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
  25. Gkazi, A.S. et al. Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation. Front. Immunol. 9: 2547 (2018).
    [DOI] [PMC]
    • SRA Accession: SRP136075
    • Species: Homo sapiens
    • Illumina MiSeq, mRNA
  26. Gomez-Tourino, I. et al. T cell receptor Beta-chains display abnormal shortening and repertoire sharing in type 1 diabetes. Nature Communications, 8;1792 (2017).
    [DOI]
    • Available from OSF: DOI 10.17605/OSF.IO/72XSZ
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  27. Harden, J.L et al. Deep sequencing of the T-cell receptor repertoire demonstrates polyclonal T-cell infiltrates in psoriasis. F1000Res, 4:460 (2015).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  28. 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
  29. Herati, R.S. et al. Successive annual influenza vaccination induces a recurrent oligoclonotypic memory response in circulating T follicular helper cells. Sci Immunol. 2(8). pii: eaag2152 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies ImmuneACCESS
  30. Henderson, L.A. et al. Next generation sequencing reveals restriction and clonotypic expansion of regulatory T cells in juvenile idiopathic arthritis. Arthritis Rheumatol. 68(7):1758-68 (2016).
    [DOI] [PubMed] [PMC]
  31. Hsu, M.S. et al. TCR Sequencing Can Identify and Track Glioma- Infiltrating T Cells after DC Vaccination. Cancer Immunology Research 4, 412 (2016).
    [DOI]
  32. 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
  33. Huth, A. et al. Antigen-Specific TCR Signatures of Cytomegalovirus Infection. J. Immunol. 202(3) (2019).
    [DOI] [PubMed]
    • SRA Accession: PRJNA473147
    • Species: Homo sapiens
    • Illumina HiSeq 1500, mRNA
  34. Jia, Q. et al. Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer. Nat. Commun. 9(1) (2018).
    [DOI] [PubMed] [PMC]
    • SRA Accession: PRJNA493023
    • Species: Homo sapiens
    • Illumina HiSeq, mRNA
  35. 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
  36. Kanakry, C.G. et al. Origin and evolution of the T-cell repertoire after posttransplantation cyclophosphamide. JCI Insight, 1(5) (2016).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  37. Kargl, J. et al. Neutrophils dominate the immune cell composition in non-small cell lung cancer. Nat. Comm. 8, 14381 (2017).
    [DOI] [PMC]
  38. 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
  39. Kooreman, N.G. et al. Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo. Cell Stem Cell, 5;22(4):501-513.e7 (2018).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Bitoechnologies
  40. 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
  41. Lang-Kuhs, K.A. et al. T cell receptor repertoire among women who cleared and failed to clear cervical human papillomavirus infection: An exploratory proof-of-principle study. PLoS ONE 13(1): e0178167 (2018).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Bitoechnologies
  42. Le, D.T. et al. Mismatch-repair deficiency predicts response of solid tumors to PD-1 blockade. Science, 357(6349):409-413 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Bitoechnologies
  43. Levine, A.J. et al. The evolution of thymic lymphomas in p53 knockout mice. Genes & Dev. 28, 2613 (2014).
    [DOI]
  44. Li, B. et al. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nature Genetics 48, 725 (2016).
    [DOI] [Adaptive Biotech] [TCGA]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  45. Li, H. et al. Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma. Cell, 176(4) (2019).
    [DOI] [PubMed]
  46. Li, Y. et al. Preliminary analysis of spatial-temporal homogeneity and heterogeneity of TCR Beta chain CDR3 repertoires in BALB/c mice. Int. J. Mol. Eidemiol. Genet. 10(1): 10–28 (2019).
    [PubMed] [PMC]
    • Species: Mus musculus
    • Adaptive Biotechnologies, mRNA
  47. 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
  48. 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
  49. 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
  50. 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
  51. Mallet, V. et al. Hepatitis E virus-induced primary cutaneous CD30(+) T cell lymphoproliferative disorder. J. Hepatol. 67(6):1334-1339 (2017).
    [DOI] [PubMed]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  52. 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]
  53. Mansfield, A.S. et al. Contraction of T cell richness in lung cancer brain metastases. Scientific Reports, 8:2171 (2018).
    [DOI]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  54. 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
  55. Mazzotti, C. Myeloma MRD by deep sequencing from circulating tumor DNA does not correlate with results obtained in the bone marrow. Blood Advances, 2:2811-2813 (2018).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  56. Migalska, M. et al. Profile of the TCR-beta repertoire in non-model species using high-throughput sequencing. Sci. reports, 8;11613 (2018).
    [DOI]
    • SRA Accession: PRJEB22487
    • Species: Myodes glareolus
    • Illumina MiSeq, mRNA
  57. Miller, N.J. et al. Tumor-Infiltrating Merkel Cell Polyomavirus-Specific T Cells Are Diverse and Associated with Improved Patient Survival. Cancer Immunol Res 5(2):137-147 (2017).
    [DOI] [PubMed] [PMC]
    • ImmunoSEQ, mRNA
    • Adaptive Biotechnologies
  58. Miron, M. et al. Human lymph nodes maintain TCF-1hi memory T cells with high functional potential and clonal diversity throughout life. J. Immunol. 201(7) (2018).
    [DOI] [PubMed]
    • SRA Accession: PRJNA416809
    • Species: Homo sapiens
    • Illumina HiSeq 2000, mRNA
  59. 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
    • Annotated sequences available on iReceptor

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HTS AIRR-Seq data sets with minimal or no data and/or do not provide public access to the original sequence files