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ADNP regulates chromatin architecture and lineage fidelity during neural differentiation

GSE303981 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 31 samples Submitted 2026/03/12 Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 31 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
31 samples: 11 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
ADNP regulates chromatin architecture and lineage fidelity during neural differentiationPLoS genetics · 2026
Summary (written by the submitters)
Activity-dependent neuroprotective protein (ADNP) is frequently mutated in autism spectrum disorder and causal in its namesake neurodevelopmental syndrome. In mouse embryonic stem cells (mESCs), ADNP forms the ChAHP complex to function in gene regulation as well as genome organization, where it competes with binding of the architectural protein CTCF.
Read the full summary ↓
However, it is unclear whether these functions persist in differentiated cells. To shed light on this question, we have established an ADNP-degron cell line to examine CTCF binding, gene expression and chromatin organization upon ADNP loss in neural progenitor cells (NPCs).
Published in
ADNP regulates chromatin architecture and lineage fidelity during neural differentiation
Wulfridge P, Rell N, Doherty J et al. · PLoS genetics 2026 · PMID 41920822 · doi:10.1371/journal.pgen.1012081
This dataset
Open GSE303981 in finder → Find more mouse 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 GSE303981_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 PRJNA1298356 and SRA study SRP604401. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41920822) ↗
Study design
11 conditions, mostly in duplicate
mESC_Control_RNA ×3 NPC_Control_RNA ×3 NPC_ASVdTAG13_RNA ×3 mESC_Control_CTCF ×2 mESC_Control_ADNP ×2 mESC_ASVdTAG13_CTCF ×2 NPC_Control_CTCF ×2 NPC_Control_ADNP ×2 +9 more

Supports a between-group comparison across 25 samples.

How we read this: 11 replicated groups read from 31 sample titles; they account for 25 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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