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Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells.

GSE267262 Mus musculus (mouse) DNA methylation 12 samples Submitted 2025/05/22 Platform GPL24247
At a glance

DNA methylation · mouse · 12 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
12 samples: 3 × DMSO_129 vs 3 × iMEK_129 vs 3 × DMSO_B6 vs 3 × iMEK_B6Groups 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
Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cellsStem cell reports · 2025
Summary (written by the submitters)
We observed markedly different DNA methylation chances in response to MAP kinase inhibition between 129 and B6J mESCs. We reasoned that these differences at least in part are driven by the differential expression of DNA methylation regulators and conducted RNA sequencing experiments.
Published in
Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naive pluripotent stem cells
Parikh C, Glenn RA, Shi Y et al. · Stem cell reports 2025 · PMID 40086447 · doi:10.1016/j.stemcr.2025.102450
This dataset
Open GSE267262 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 GSE267262_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1110767 and SRA study SRP507195. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40086447) ↗
Study design
3 × DMSO_129 vs 3 × iMEK_129 vs 3 × DMSO_B6 vs 3 × iMEK_B6

Supports a between-group comparison across 12 samples.

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
Datasets on a similar topic

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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.