T cell fate and clonality inference from single-cell transcriptomes

The TraCeR tool extracts full-length, paired T cell receptor sequences from single-cell RNA-sequencing data from T lymphocytes, enabling a combination of clonotype and functional analysis. 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.