title: 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.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
authors.forename: Michael J T
authors.initials: MJT
authors.lastname: Stubbington
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
authors.forename: Tapio
authors.initials: T
authors.lastname: Lönnberg
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
authors.forename: Valentina
authors.initials: V
authors.lastname: Proserpio
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Clare
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Anneliese O
authors.initials: AO
authors.lastname: Speak
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.|Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Teichmann
mesh_terms: D000818:Animals; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology / Q000378:metabolism* / Q000473:pathology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008213:Lymphocyte Activation; D051379:Mice; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D012475:Salmonella / Q000235:genetics; D012481:Salmonella Infections, Animal / Q000235:genetics / Q000276:immunology*; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D011948:Receptors, Antigen, T-Cell