GEO series
H2A.Z regulates memory CD8+ T cell recall response [4]
GSE273195
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
34 samples
Submitted 2025/07/29
Platform GPL24247
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 34 samples: 17 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- H2A.Z primes an epigenetic landscape for memory CD8(+) T cell recall responseNature communications · 2025
Summary (written by the submitters)
The rapid response of memory CD8+ T cells is crucial for the body's defense against infection and cancer. However, the mechanisms underlying memory recall responses remain unclear. Here we show that the rapid response of memory T cells is accompanied by the induction of gene expression associated with memory CD8+ T cell activation-recalled genes, which participate in various biological functions, such as response to antigen signals, intracellular phosphorylation kinase signaling pathways, and cytokine production.
Read the full summary ↓
And the expression of ARGs in memory T cells is closely associated with their epigenetic features. We found that the genomic loci of ARGs in memory T cells exhibit active epigenetic marks, such as increased H2A.Z binding, elevated levels of H3K27 acetylation, enhanced binding of Pol II S5P, and reduced levels of repressive histone mark H3K27me3. Interestingly, H2A.Z plays a crucial role in modulating these epigenetic features. Depletion of H2A.Z results in a reduction in H3K27ac levels, decreased binding of Pol II, increased levels of H3K27me3, and a decrease in chromatin accessibility. Functionally, H2A.Z is essential in quiescent memory CD8+ T cells for generating effector CD8+ T cells, producing effector molecules and effectively eliminating pathogens during recall responses. In addition, H2A.Z deposition at specific ARG gene loci in the genome is mainly regulated by TCR/CD28 signals, and may be partly regulated by IL-7 and IL-15. Overall, these findings demonstrate that H2A.Z orchestrates the epigenetic landscape at ARG gene loci to regulate the recall responses of memory T cells.
Published in
Liang W, Ding J, Chai Q et al.
· Nature communications 2025
· PMID 40817373
· doi:10.1038/s41467-025-62976-4
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE273195_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1140587 and SRA study SRP522436. Searching any of these in the dataset finder brings you back here.
Study design
17 conditions, mostly in duplicate
TN_PolIIS5P-CUTandTag ×2
TM_PolIIS5P-CUTandTag ×2
TN_H2A.Z-CUTandTag ×2
WT-TM_H2A.Z-CUTandTag ×2
cKO-TM_H2A.Z-CUTandTag ×2
WT-TM_ATAC-seq ×2
cKO-TM_ATAC-seq ×2
WT-TM_H3K4me3-CUTandTag ×2
+9 more
Supports a between-group comparison across 34 samples.
How we read this: 17 replicated groups read from 34 sample titles; they account for 34 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM8423863 TN_PolIIS5P-CUTandTag_rep1 TN_PolIIS5P-CUTandTag
- GSM8423864 TN_PolIIS5P-CUTandTag_rep2 TN_PolIIS5P-CUTandTag
- GSM8423865 TM_PolIIS5P-CUTandTag_rep1 TM_PolIIS5P-CUTandTag
- GSM8423866 TM_PolIIS5P-CUTandTag_rep2 TM_PolIIS5P-CUTandTag
- GSM8423867 TN_H2A.Z-CUTandTag_rep1 TN_H2A.Z-CUTandTag
- GSM8423868 TN_H2A.Z-CUTandTag_rep2 TN_H2A.Z-CUTandTag
- GSM8423869 WT-TM_H2A.Z-CUTandTag_rep1 WT-TM_H2A.Z-CUTandTag
- GSM8423870 WT-TM_H2A.Z-CUTandTag_rep2 WT-TM_H2A.Z-CUTandTag
- GSM8423871 cKO-TM_H2A.Z-CUTandTag_rep1 cKO-TM_H2A.Z-CUTandTag
- GSM8423872 cKO-TM_H2A.Z-CUTandTag_rep2 cKO-TM_H2A.Z-CUTandTag
- GSM8423873 WT-TM_ATAC-seq_rep1 WT-TM_ATAC-seq
- GSM8423874 WT-TM_ATAC-seq_rep2 WT-TM_ATAC-seq
- GSM8423875 cKO-TM_ATAC-seq_rep1 cKO-TM_ATAC-seq
- GSM8423876 cKO-TM_ATAC-seq_rep2 cKO-TM_ATAC-seq
- GSM8423877 WT-TM_H3K4me3-CUTandTag_rep1 WT-TM_H3K4me3-CUTandTag
- GSM8423878 WT-TM_H3K4me3-CUTandTag_rep2 WT-TM_H3K4me3-CUTandTag
- GSM8423879 cKO-TM_H3K4me3-CUTandTag_rep1 cKO-TM_H3K4me3-CUTandTag
- GSM8423880 cKO-TM_H3K4me3-CUTandTag_rep2 cKO-TM_H3K4me3-CUTandTag
- GSM8423881 WT-TM_H3K27me3-CUTandTag_rep1 WT-TM_H3K27me3-CUTandTag
- GSM8423882 WT-TM_H3K27me3-CUTandTag_rep2 WT-TM_H3K27me3-CUTandTag
- GSM8423883 cKO-TM_H3K27me3-CUTandTag_rep1 cKO-TM_H3K27me3-CUTandT…
- GSM8423884 cKO-TM_H3K27me3-CUTandTag_rep2 cKO-TM_H3K27me3-CUTandT…
- GSM8423885 WT-TM_PolIIS5P-CUTandTag_rep1 WT-TM_PolIIS5P-CUTandTag
- GSM8423886 WT-TM_PolIIS5P-CUTandTag_rep2 WT-TM_PolIIS5P-CUTandTag
- GSM8423887 cKO-TM_PolIIS5P-CUTandTag_rep1 cKO-TM_PolIIS5P-CUTandT…
- GSM8423888 cKO-TM_PolIIS5P-CUTandTag_rep2 cKO-TM_PolIIS5P-CUTandT…
- GSM8423889 WT-TM_Input-ChIP-seq_rep1 WT-TM_Input-ChIP-seq
- GSM8423890 WT-TM_Input-ChIP-seq_rep2 WT-TM_Input-ChIP-seq
- GSM8423891 cKO-TM_Input-ChIP-seq_rep1 cKO-TM_Input-ChIP-seq
- GSM8423892 cKO-TM_Input-ChIP-seq_rep2 cKO-TM_Input-ChIP-seq
- GSM8423893 WT-TM_H3K27ac-ChIP-seq_rep1 WT-TM_H3K27ac-ChIP-seq
- GSM8423894 WT-TM_H3K27ac-ChIP-seq_rep2 WT-TM_H3K27ac-ChIP-seq
- GSM8423895 cKO-TM_H3K27ac-ChIP-seq_rep1 cKO-TM_H3K27ac-ChIP-seq
- GSM8423896 cKO-TM_H3K27ac-ChIP-seq_rep2 cKO-TM_H3K27ac-ChIP-seq
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Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.