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Series GSE184260 Query DataSets for GSE184260
Status Public on Jun 30, 2023
Title ATAC-Seq of CD4+ T cell subsets during LCMV infection
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Following an infection, CD4+ lymphocytes can differentiate into long-lived memory T cells, some of which circulate through the secondary lymphoid organs (SLOs) while a population lodges in non-lymphoid tissues. While CD4+ T cells in SLOs have been examined, the developmental origins and transcriptional regulation of tissue-resident memory T cells (TRM) remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profile of virus-specific CD4+ TRM in the small intestine (SI) following acute lymphocytic choriomeningitis virus (LCMV) infection. LCMV-specific CD4+ TRM at day 7 of infection shared a gene-expression program and chromatin profile with TH1 cells and progressively acquired a mature TRM program by day 21 memory time point, supporting a developmental relationship between TRM and TH1 subsets. Furthermore, we demonstrated that TRM cells expressed genes associated with both effector and memory T cell fates, including the transcriptional regulators Blimp1, Id2, and Bcl6 which were necessary for CD4+ TRM differentiation. TH1-associated Blimp1 and Id2 were both required for early TRM formation, while TFH-associated Bcl6 initially inhibited TRM differentiation but was critical for development of long-lived TRM cells. Our results identify new significance for TFs previously associated with circulating CD4+ T cell populations and their roles in driving SI CD4+ TRM differentiation.
Overall design 6 samples, 2 replicates each, Day 7 or Day 20 LCMV infection CD4+ T cell subsets
Contributor(s) Nguyen QP, Deng TZ, Goldrath AW
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Submission date Sep 16, 2021
Last update date Jun 30, 2023
Contact name Ananda Goldrath
Organization name UCSD
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093-0377
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM5582645 D7_IEL_Rep1
GSM5582646 D7_IEL_Rep2
GSM5582647 D7_LPL_Rep1
This SubSeries is part of SuperSeries:
GSE184263 CD4+ T cell subsets during LCMV infection
BioProject PRJNA763854
SRA SRP337409

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Supplementary file Size Download File type/resource 2.2 Mb (ftp)(http) BB 4.4 Mb (ftp)(http) BB 2.6 Mb (ftp)(http) BB 1.8 Mb (ftp)(http) BB 2.4 Mb (ftp)(http) BB 3.4 Mb (ftp)(http) BB
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