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Nat Methods. 2016 Apr;13(4):329-332. doi: 10.1038/nmeth.3800. Epub 2016 Mar 7.

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

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
2
Wellcome Trust Sanger Institute, Cambridge, UK.
#
Contributed equally

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.

PMID:
26950746
PMCID:
PMC4835021
DOI:
10.1038/nmeth.3800
[Indexed for MEDLINE]
Free PMC Article

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