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T cell fate and clonality inference from single-cell transcriptomes.

ABSTRACT: We developed TraCeR, a computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. We found that T cell clonotypes in a mouse Salmonella infection model span early activated CD4(+) T cells as well as mature effector and memory cells.

SUBMITTER: Stubbington MJT

PROVIDER: S-EPMC4835021 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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T cell fate and clonality inference from single-cell transcriptomes.

Stubbington Michael J T MJT Lönnberg Tapio T Proserpio Valentina V Clare Simon S Speak Anneliese O AO Dougan Gordon G Teichmann Sarah A SA

Nature methods 20160307 4

We developed TraCeR, a computational method to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. TraCeR links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. We found that T cell clonotypes in a mouse Salmonella infection model span early activated CD4(+) T cells as well as mature effector and memory cells. ...[more]

PMID: 26950746

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