T cell fate and clonality inference from single-cell transcriptomes.
Accepted version
Peer-reviewed
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Authors
Stubbington, Michael JT
Lönnberg, Tapio
Proserpio, Valentina
Clare, Simon
Speak, Anneliese O
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.
Description
Keywords
Animals, CD4-Positive T-Lymphocytes, High-Throughput Nucleotide Sequencing, Lymphocyte Activation, Mice, Receptors, Antigen, T-Cell, Salmonella, Salmonella Infections, Animal, Single-Cell Analysis, Software, Transcriptome
Journal Title
Nat Methods
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Journal ISSN
1548-7091
1548-7105
1548-7105
Volume Title
13
Publisher
Springer Science and Business Media LLC
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All rights reserved