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.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Animals
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CD4-Positive T-Lymphocytes / immunology
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CD4-Positive T-Lymphocytes / metabolism*
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CD4-Positive T-Lymphocytes / pathology
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High-Throughput Nucleotide Sequencing / methods*
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Lymphocyte Activation
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Mice
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Receptors, Antigen, T-Cell / genetics*
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Salmonella / genetics
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Salmonella Infections, Animal / genetics
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Salmonella Infections, Animal / immunology*
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Single-Cell Analysis / methods*
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Software*
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Transcriptome*
Substances
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Receptors, Antigen, T-Cell