← BioTransfer GEO Dataset Finder
GEO series

Neural stem cells epigenomes and fate bias are temporally coordinated during corticogenesis [scATAC-seq]

GSE292319 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2026/06/10 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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
10 samples: 5 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
Neural stem cell epigenomes and fate bias are temporally coordinated during mouse cortical developmentGenes & development · 2026
Summary (written by the submitters)
The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell transcriptomics and chromatin accessibility, together with genome-wide profiling of DNA methylation and 3D chromosomal contact across mouse corticogenesis (E13–E18) to elucidate cell fate transitions.
Read the full summary ↓
We reveal using metacell flow analysis that neural stem cells (NSC) progressively shift from an intermediate progenitor–biased state toward an astrocytic lineage and that his process is accompanied with DNA methylation programming and chromosomal insulation changes. A model integrating transcription factor motif affinities with epigenetic features, identifies key regulators of cis-regulatory element (CRE) activation. In vivo reporter assays further decouple the intrinsic regulatory potential of CREs from context-dependent synergistic activation. Collectively, our findings uncover temporal epigenomic reprogramming that underlies the evolving differentiation potential of NSC, providing insights into the intrinsic and extrinsic mechanisms that pattern cortical lineages.
Published in
Neural stem cell epigenomes and fate bias are temporally coordinated during mouse cortical development
Shapira Y, Noack F, Vangelisti S et al. · Genes & development 2026 · PMID 42020311 · doi:10.1101/gad.353090.125
This dataset
Open GSE292319 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 GSE292319_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 PRJNA1237904 and SRA study SRP571421. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42020311) ↗
Study design
5 conditions, mostly in duplicate
scATAC-seq in E13 somatosensory mouse cortex ×2 scATAC-seq in E15 somatosensory mouse cortex ×2 scATAC-seq in E16 somatosensory mouse cortex ×2 scATAC-seq in E17 somatosensory mouse cortex ×2 scATAC-seq in E18 somatosensory mouse cortex ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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 ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.