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A conserved function of EZH2-PRC2 in the repression of primitive endoderm cell fate [RNA-Seq - mouse]

GSE291454 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2026/01/14 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 22 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
Mus musculus (mouse)
Samples
22 samples: 10 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
A conserved function of EZH2-PRC2 in repression of primitive endoderm fate in mouse and human pluripotent cellsStem cell reports · 2025
Summary (written by the submitters)
In early blastocyst, inner cell mass (ICM) initiates the second wave of cell fate decisions to generate epiblast and primitive endoderm (PrE), crucial for proper embryo development. However, the epigenetic mechanisms underlying this segregation remain incompletely understood. Here, we reveal that treatment of embryonic stem cells (ESCs) with the EZH2 inhibitor EPZ-6438 significantly enhances transdifferentiation efficiency from ESCs to primitive endoderm stem cells (PrESCs).
Read the full summary ↓
EZH2 knockout in ESCs markedly reduces H3K27me3 modification near the promoter regions of PrE-specific genes, upregulating their expression and promoting transition to PrESCs. Overexpression of wildtype EZH2, but not catalytic site or EED-binding motif mutants, prevents this transition. Notably, the ICM of mouse blastocysts treated with EPZ6438 at 8-cell stage contain almost no epiblast but only GATA6 positive cells. Finally, EPZ6438 treatment in human naïve ESCs upregulates hypoblast-associated genes. These findings demonstrated the conserved function of EZH2-PRC2 in protecting the pluripotency from primitive endoderm cell fate.
Published in
A conserved function of EZH2-PRC2 in repression of primitive endoderm fate in mouse and human pluripotent cells
Chen J, Huang B, Zhai X et al. · Stem cell reports 2025 · PMID 41173005 · doi:10.1016/j.stemcr.2025.102689
This dataset
Open GSE291454 in finder → Find more mouse 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 GSE291454_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 PRJNA1233787 and SRA study SRP568973. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41173005) ↗
Study design
10 conditions, mostly in duplicate
ESC ×3 EZH2KO.10SL ×3 C57.ESC ×2 C57.PrESC ×2 EPZ.iPrE1 ×2 EPZ.iPrE2 ×2 TG2A.NG.PB.ESC ×2 EZH2KO.10SL.rescued ×2 +2 more

Supports a between-group comparison across 22 samples.

How we read this: 10 replicated groups read from 22 sample titles; they account for 22 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
Datasets on a similar topic

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