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Epigenetically controlled ZEB2 expression promotes the cytotoxic potential of CMV-specific CD8+ T cells

GSE291537 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/12/04 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
12 samples: 3 × CD8+ effector T cells, scrambled control, experiment 1, dono vs 3 × CD8+ effector T cells, scrambled control, experiment 2, dono vs 3 × CD8+ effector T cells, ZEB2 knockout, experiment 1, dono vs 3 × CD8+ effector T cells, ZEB2 knockout, experiment 2, donoGroups 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
Epigenetically Controlled ZEB2 Expression Promotes the Cytotoxic Potential of CMV-Specific CD8(+) T CellsEuropean journal of immunology · 2025
Summary (written by the submitters)
Zinc finger E-box binding protein 2 (ZEB2) is a key factor in the differentiation of naive CD8+ T cells into effector and memory T cells. However, the precise regulatory role of ZEB2 in cytotoxic CD8+ T cells remains unknown. Our recent DNA methylation analysis of cytomegalovirus (CMV)-specific human CD8+ T cells revealed two differentially methylated regions (DMRs) within the ZEB2 locus.
Read the full summary ↓
We showed that these ZEB2 DMRs undergo pronounced demethylation during T cell differentiation. In particular, terminally differentiated CD8+ T cells and cytotoxic CD4+ T cells show almost complete demethylation. A ZEB2 knockout approach in CD8+ effector T cells followed by RNA-seq analysis revealed an altered gene expression profile, affecting genes related to cell-cell adhesion and impairing cytotoxicity in CMV-specific killing assays. Our data show that ZEB2 expression contributes to the differentiation of naive CD8+ T cells into effector and memory T cells and regulates the functional properties of virus-specific cytotoxic CD8+ T cells.
Published in
Epigenetically Controlled ZEB2 Expression Promotes the Cytotoxic Potential of CMV-Specific CD8(+) T Cells
Sasidharan Nair V, Yu Z, Ahmadi H et al. · European journal of immunology 2025 · PMID 41195865 · doi:10.1002/eji.70084
This dataset
Open GSE291537 in finder → Find more human RNA-seq datasets →
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.

Series matrix ↓
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 GSE291537_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
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.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1234107 and SRA study SRP569149. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41195865) ↗
Study design
3 × CD8+ effector T cells, scrambled control, experiment 1, dono vs 3 × CD8+ effector T cells, scrambled control, experiment 2, dono vs 3 × CD8+ effector T cells, ZEB2 knockout, experiment 1, dono vs 3 × CD8+ effector T cells, ZEB2 knockout, experiment 2, dono

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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