Characterization of CD8 T cells during acute LCMV infection using scRNA-seq

UID: 10982

Author(s): Cui, Weiguo, Schauder, David M.

Description: Summary from GEO:

"During a viral infection, CD8 T cells encounter a myriad of antigenic and inflammatory signals of variable strength, which sets off each individual T cell on a unique differentiation trajectory. However, the developmental path for each of these cells will ultimately lead to one of only two potential outcomes after clearance of the infection—death or survival and development into memory CD8 T cells. How this cell fate decision is made remains incompletely understood. In this study, we explore the dynamic transcriptional changes during effector and memory CD8 T cell differentiation at the single cell level."

Overall design from GEO:

"Three samples (Day 0, 9, and 129) prepared using 10x Genomics Chromium platform."

Subject of Study

Subject(s)

Access via GEO

Accession #: GSE130130

Access via BioProject

Accession #: PRJNA534058

Access via SRA

Accession #: SRP193322
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, BioProject, and SRA databases provide open access to these files.
Associated Publications: Gearty S, Dündar F, Zumbo P, Espinosa-Carrasco G, Shakiba M, Sanchez-Rivera F, Socci N, Trivedi P, Lowe S, Lauer P, Mohibullah N, Viale A, DiLorenzo T, Betel D, Schietinger A. An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature. 2022; 602(7895):156-161.

Schauder DM, Shen J, Chen Y, Kasmani MY, Kudek MR, Burns R, Cui W. E2A-regulated epigenetic landscape promotes memory CD8 T cell differentiation. Proc Natl Acad Sci U S A. 2021 Apr 20;118(16):e2013452118. PMID: 33859041; PMCID: PMC8072256.
Equipment Used: 10X Chromium
10x Genomics' Chromium technology partitions reactions into nanoliter-scale droplets containing uniquely barcoded beads called GEMs (Gel Bead-In EMulsions). This core technology can be used to partition single cells, nuclei, or high molecular weight gDNA to prepare next generation sequencing libraries in parallel.

Illumina NextSeq 500
Dataset Format(s): TSV, TAR, MTX
Dataset Size: 14 MB

Do you have or know of a dataset that should be added to the catalog? Let us know!