GSE136028 TCR sequencing paired with massively parallel 3 ′ RNA-seq reveals clonotypic T cell signatures

Contributors : Ang A Tu ; Todd M Gierahn ; Brinda Monian ; Duncan M Morgan ; Naveen K Mehta ; Bert Ruiter ; Wayne G Shreffler ; Alex K Shalek ; J C LoveSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHigh-throughput 3 ′ single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individualimmune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features,including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy thatenables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3 ′-barcoded scRNA-seq samples.This approach is compatible with common 3 ′ scRNA-seq methods, and adaptable to processed samples post hoc. We appliedthe technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice andfrom patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studyingdiseases in which clonotype-driven responses are critical to understanding the underlying biology.
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

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