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| Status |
Public on Nov 19, 2019 |
| Title |
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
High-throughput 3′ single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune 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 that enables 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 applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.
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| Overall design |
Single-cell RNA-Sequencing of murine samples via Seq-Well. Mouse 1-4 was sorted against HPV-E7 peptide (RAHYNIVTF) MHC-tetramer. OT1 (spiked into wild-type BL6 murine T cells) samples were enriched for T cells using magnetic beads enrichment, without MHC-tetramer sorting. See DOI: 10.1038/s41590-019-0544-5.
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| Contributor(s) |
Tu AA, Gierahn TM, Monian B, Morgan DM, Mehta NK, Ruiter B, Shreffler WG, Shalek AK, Love JC |
| Citation(s) |
31745340 |
| Submission date |
Aug 19, 2019 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Ang Andy Tu |
| E-mail(s) |
andytu@alum.mit.edu
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biological Engineering
|
| Lab |
J. Christopher Love
|
| Street address |
500 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA560970 |
| SRA |
SRP218863 |
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