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DNA Crosslink-induced Transcriptional Changes in Mouse Embryonic Stem Cells

GSE297363 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/05/26 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 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
Mus musculus (mouse)
Samples
12 samples: 3 × FANCMMMC vs 3 × FANCMNT vs 3 × WTMMC vs 3 × WTNTGroups 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
Embryonic Stem Cell-Specific Responses to DNA Replication StressbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Genome maintenance is of the utmost importance in stem cells, as mutations can be propagated and cause defects in derivative tissues. Many stem cell types display low mutation rates, with embryonic stem cells (ESCs) being a notable example. The bases for this property are unclear but may be achieved by optimization of various processes including high-fidelity DNA repair, cell cycle checkpoint controls, and hypersensitivity to genotoxic insults that trigger cell death.
Read the full summary ↓
Here, we investigate the transcriptional basis of the unique responses of mouse ESCs (mESCs) to replication stress (RS) using MMC. We find that whereas mESCs lack a strong G2/M checkpoint, they maintain a spindle assembly checkpoint (SAC).
Published in
Embryonic Stem Cell-Specific Responses to DNA Replication Stress
James RC, Wang JK, Bhatt SR et al. · bioRxiv : the preprint server for biology 2025 · PMID 40463205 · doi:10.1101/2025.05.16.654332
This dataset
Open GSE297363 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 GSE297363_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 PRJNA1264058 and SRA study SRP586124. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40463205) ↗
Study design
3 × FANCMMMC vs 3 × FANCMNT vs 3 × WTMMC vs 3 × WTNT

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

Search all mouse RNA-seq datasets in GEO →

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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.