GEO series
HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection
GSE255887
Mus musculus
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
76 samples
Submitted 2025/05/22
Platform GPL24247
Summary
CD8+ T cell exhaustion is a complex process involving the differentiation of persistently acti-vated CD8+ T cells into functionally distinct cell subsets. Here, we investigated the role of the key epigenetic regulator histone deacetylase 1 (HDAC1) in the differentiation of exhausted T (Tex) cells during chronic viral infection. We uncovered that HDAC1 controls the generation and maintenance of effector-like CX3CR1+ Tex cells in a CD8+ T cell-intrinsic manner. Dele-tion of HDAC1 led to expansion of an alternative Tex subset characterized by high expression of T cell exhaustion markers, and this was accompanied by elevated viremia. HDAC1 bound to and facilitated an open chromatin state of effector-like signature gene loci in progenitor Tex cells, thereby priming cell fate specification toward the CX3CR1+ Tex subset. Our study un-covers a selective role for HDAC1 in CX3CR1+ Tex subset differentiation, which is essential for controlling viral load during chronic infection.
Published in
Rica R, Waldherr M, Miyakoda E et al.
· The Journal of experimental medicine 2025
· PMID 40464916
· doi:10.1084/jem.20240829
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE255887_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 76 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1076916 and SRA study SRP490082. Searching any of these in the dataset finder brings you back here.
Study design
36 conditions, each sampled once — no replicated groups
mouse, WT, early-TexProg, HDAC1, biol ×2
mouse, WT, early-TexProg, H3K27ac, biol ×2
mouse, WT, early-TexProg, Runx3, biol ×2
mouse, WT, early-TexProg, H3K27me3, biol ×2
Read from the first 40 of 76 sample titles: 36 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8082209 CD8+ Tcells, Wildtype, Tprog, Replicate 1, ATACseq
- GSM8082210 CD8+ Tcells, Wildtype, Tprog, Replicate 2, ATACseq
- GSM8082211 CD8+ Tcells, Wildtype, Tprog, Replicate 3, ATACseq
- GSM8082212 CD8+ Tcells, Wildtype, Tterm, Replicate 1, ATACseq
- GSM8082213 CD8+ Tcells, Wildtype, Tterm, Replicate 2, ATACseq
- GSM8082214 CD8+ Tcells, Wildtype, Tterm, Replicate 3, ATACseq
- GSM8082215 CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 1, ATACseq
- GSM8082216 CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 2, ATACseq
- GSM8082217 CD8+ Tcells, HDAC1-cKO, Tprog, Replicate 3, ATACseq
- GSM8082218 CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 1, ATACseq
- GSM8082219 CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 2, ATACseq
- GSM8082220 CD8+ Tcells, HDAC1-cKO, Tterm, Replicate 3, ATACseq
- GSM8082243 CD8+ Tcells, Biol. Replicate 1, scRNAseq
- GSM8082244 CD8+ Tcells, Biol. Replicate 1, scRNAseq HTO
- GSM8082245 CD8+ Tcells, Biol. Replicate 2, scRNAseq
- GSM8082246 CD8+ Tcells, Biol. Replicate 2, scRNAseq HTOP
- GSM8981712 mouse, WT, early-TexProg, HDAC1, biol rep1
- GSM8981713 mouse, WT, early-TexProg, H3K27ac, biol rep1
- GSM8981714 mouse, WT, early-TexProg, Runx3, biol rep1
- GSM8981715 mouse, WT, early-TexProg, H3K27me3, biol rep1
- GSM8981716 mouse, WT, early-TexProg, IgG, biol rep1
- GSM8981717 mouse, HDAC1-cKO, early-TexProg, HDAC1, biol rep1
- GSM8981718 mouse, HDAC1-cKO, early-TexProg, H3K27ac, biol rep1
- GSM8981719 mouse, HDAC1-cKO, early-TexProg, Runx3, biol rep1
- GSM8981720 mouse, HDAC1-cKO, early-TexProg, H3K27me3, biol rep1
- GSM8981721 mouse, HDAC1-cKO, early-TexProg, IgG, biol rep1
- GSM8981722 mouse, WT, early-non-TexProg, HDAC1, biol rep1
- GSM8981723 mouse, WT, early-non-TexProg, H3K27ac, biol rep1
- GSM8981724 mouse, WT, early-non-TexProg, Runx3, biol rep1
- GSM8981725 mouse, WT, early-non-TexProg, H3K27me3, biol rep1
- GSM8981726 mouse, WT, early-non-TexProg, IgG, biol rep1
- GSM8981727 mouse, HDAC1-cKO, early-non-TexProg, HDAC1, biol rep1
- GSM8981728 mouse, HDAC1-cKO, early-non-TexProg, H3K27ac, biol rep1
- GSM8981729 mouse, HDAC1-cKO, early-non-TexProg, Runx3, biol rep1
- GSM8981730 mouse, HDAC1-cKO, early-non-TexProg, H3K27me3, biol rep1
- GSM8981731 mouse, HDAC1-cKO, early-non-TexProg, IgG, biol rep1
- GSM8981732 mouse, WT, early-TexProg, HDAC1, biol rep2
- GSM8981733 mouse, WT, early-TexProg, H3K27ac, biol rep2
- GSM8981734 mouse, WT, early-TexProg, Runx3, biol rep2
- GSM8981735 mouse, WT, early-TexProg, H3K27me3, biol rep2
+ 36 more — browse all 76 samples with per-sample file links →
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