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Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [CUT&Run]

GSE298002 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 38 samples Submitted 2025/11/28 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 38 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
38 samples: 14 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
Stage-specific epigenetic priming amplifies gene activation during lineage commitmentScience advances · 2026
Summary (written by the submitters)
Precise regulation of epigenetic marks is critical for proper lineage commitment throughout neurodevelopment. Mutations in members of the MSL acetyltransferase complex (MSLc), specific for H4K16ac, are associated with neurodevelopmental disorders in humans. However, the precise gene targets and enzymatic contributions of the MSLc during neural differentiation remain unclear.
Read the full summary ↓
Through single-cell multi-omics analysis, we demonstrate that Msl1 deletion leads to severe neurodevelopmental defects, culminating in embryonic lethality by E10.5. Using a rapid depletion system, we uncoupled acute transcriptional effects from epigenetic memory and found that MSLc-mediated gene priming is responsible for faithful upregulation of crucial neurodevelopmental gene programs. The priming of the MSLc target genes is limited to the initial stages of differentiation following neuronal induction, where the MSLc facilitates chromatin accessibility at regulatory regions to, allowing for selective enhancer-promoter interactions and subsequent gene activation. Our study identifies the MSLc as a crucial epigenetic regulator during neurodevelopment, providing molecular insights into MSLc-associated developmental disorders.
Published in
Stage-specific epigenetic priming amplifies gene activation during lineage commitment
Foertsch A, Hirsch N, Seyfferth J et al. · Science advances 2026 · PMID 41894493 · doi:10.1126/sciadv.adz8889
This dataset
Open GSE298002 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE298002_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1267101 and SRA study SRP587371. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41894493) ↗
Study design
14 conditions, mostly in duplicate
CUTRUN, NPC, ctrl, MSL1-V5, ×2 CUTRUN, NPC, ctrl, MSL2, ×2 CUTRUN, NPC, ctrl, MOF, ×2 CUTRUN, NPC, ctrl, H4K16ac, ×2 CUTRUN, NPC, 24h Auxin treated, MSL1-V5, ×2 CUTRUN, NPC, 24h Auxin treated, MSL2, ×2 CUTRUN, NPC, 24h Auxin treated, MOF, ×2 CUTRUN, NPC, 24h Auxin treated, H4K16ac, ×2 +16 more

Supports a case/control comparison: 12 samples read as cases, 14 as controls.

How we read this: 14 replicated groups read from 38 sample titles; they account for 28 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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