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Series GSE136028 Query DataSets for GSE136028
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.
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.
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
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
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM4039590 Mouse1_Stimulated
GSM4039591 Mouse2_Stimulated
GSM4039592 Mouse3_Stimulated
BioProject PRJNA560970
SRA SRP218863

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136028_E7_Seurat.rds.gz 110.1 Mb (ftp)(http) RDS
GSE136028_E7s_Seurat.rds.gz 107.2 Mb (ftp)(http) RDS
GSE136028_Hyporeactive_Seurat.rds.gz 27.2 Mb (ftp)(http) RDS
GSE136028_P77_seurat.Rds.gz 17.2 Mb (ftp)(http) RDS
GSE136028_RAW.tar 42.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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