publication . Article . Other literature type . 2016

T cell fate and clonality inference from single-cell transcriptomes

Valentina Proserpio; Sarah A. Teichmann; Sarah A. Teichmann; Gordon Dougan; Michael J. T. Stubbington; Tapio Lönnberg; Anneliese O. Speak; Simon Clare;
Open Access
  • Published: 07 Mar 2016 Journal: Nature Methods, volume 13, pages 329-332 (issn: 1548-7091, eissn: 1548-7105, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
  • Country: United Kingdom
Abstract
The enormous sequence diversity within T cell receptor (TCR) repertoires allows specific TCR sequences to be used as lineage markers for T cells that derive from a common progenitor. We have developed a computational method, called TraCeR, to reconstruct full-length, paired TCR sequences from T lymphocyte single-cell RNA-seq by combining existing assembly and alignment programs with “combinatorial recombinome” sequences comprising all possible TCR combinations. We validate this method to quantify its accuracy and sensitivity. Inferred TCR sequences reveal clonal relationships between T cells whilst the cells’ complete transcriptional landscapes can be quantified...
Subjects
free text keywords: Article, CD4-Positive T-Lymphocytes, Animals, Mice, Salmonella, Salmonella Infections, Animal, Receptors, Antigen, T-Cell, Lymphocyte Activation, Software, High-Throughput Nucleotide Sequencing, Transcriptome, Antigen, T cell, medicine.anatomical_structure, medicine, Biology, Cell, Genetics, Single-cell analysis, T lymphocyte, Acquired immune system, Cell biology, T-cell receptor
Funded by
WT
Project
  • Funder: Wellcome Trust (WT)
,
EC| ThDEFINE
Project
ThDEFINE
Re(defining) CD4+ T Cell Identities One Cell at a Time
  • Funder: European Commission (EC)
  • Project Code: 646794
  • Funding stream: H2020 | ERC | ERC-COG
,
EC| THSWITCH
Project
THSWITCH
Decoding genetic switches in T helper cell differentiation
  • Funder: European Commission (EC)
  • Project Code: 260507
  • Funding stream: FP7 | SP2 | ERC
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