T cell fate and clonality inference from single-cell transcriptomes

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CD4-Positive T-Lymphocytes / immunology
  • CD4-Positive T-Lymphocytes / metabolism*
  • CD4-Positive T-Lymphocytes / pathology
  • High-Throughput Nucleotide Sequencing / methods*
  • Lymphocyte Activation
  • Mice
  • Receptors, Antigen, T-Cell / genetics*
  • Salmonella / genetics
  • Salmonella Infections, Animal / genetics
  • Salmonella Infections, Animal / immunology*
  • Single-Cell Analysis / methods*
  • Software*
  • Transcriptome*


  • Receptors, Antigen, T-Cell