Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE
    • Publication Information:
      Original Publication: [London] : BioMed Central
    • Subject Terms:
      Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor* ; Gene Rearrangement, beta-Chain T-Cell Antigen Receptor*; RNA, Messenger/*genetics ; Receptors, Antigen, T-Cell, alpha-beta/*genetics ; Sequence Analysis, RNA/*methods ; Single-Cell Analysis/*methods; Adaptive Immunity ; Animals ; Gene Expression Regulation ; Humans ; Jurkat Cells ; Mice ; RNA, Messenger/immunology ; Receptors, Antigen, T-Cell, alpha-beta/immunology ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology ; V(D)J Recombination
    • Abstract:
      Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments. Source code is available at https://github.com/ElementoLab/scTCRseq .
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    • Grant Information:
      R01 CA194547 United States CA NCI NIH HHS; T32 GM083937 United States GM NIGMS NIH HHS
    • Molecular Sequence:
      GEO GSE45428
    • Accession Number:
      0 (RNA, Messenger)
      0 (Receptors, Antigen, T-Cell, alpha-beta)
    • Publication Date:
      Date Created: 20160728 Date Completed: 20170306 Latest Revision: 20181113
    • Publication Date:
      20240829
    • Accession Number:
      PMC4962388
    • Accession Number:
      10.1186/s13073-016-0335-7
    • Accession Number:
      27460926