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CHD3 regulates BMP signalling response during cranial neural crest cell specification

GSE288669 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2025/02/05 Platform GPL34284Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 56 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
Homo sapiens (human)
Samples
56 samples: 56 samples, each with a distinct title — no replicated groupsGroups 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
The NuRD component CHD3 promotes BMP signalling during cranial neural crest cell specificationEMBO reports · 2025
Summary (written by the submitters)
CHD3 is a component of the NuRD chromatin remodeller. Mutations in CHD3 cause Snijders Blok-Campeau Syndrome, a neurodevelopmental disorder marked by intellectual disability and craniofacial abnormalities. To unveil the role of CHD3 in craniofacial development, we differentiated CHD3-null induced pluripotent stem cells (iPSCs) into cranial neural crest cells (CNCC).
Read the full summary ↓
We found that CHD3 expression is low in iPSCs and neuroectoderm, but it is upregulated during CNCC specification, where CHD3-containing NuRD opens the chromatin at BMP-responsive enhancers, to allow binding of DLX5 and other factors. CHD3 loss leads to repression of BMP target genes and imbalance between BMP and Wnt signalling, which ultimately results in aberrant mesodermal fate. Consequently, cranial neural crest specification fails, replaced by mesodermal identity, which can be partially rescued by titrating Wnt levels. Our findings highlight a novel role for CHD3 as pivotal regulator of BMP signalling, essential for proper neural crest specification and craniofacial development.
Published in
The NuRD component CHD3 promotes BMP signalling during cranial neural crest cell specification
Mitchell ZH, den Hoed J, Claassen W et al. · EMBO reports 2025 · PMID 40835974 · doi:10.1038/s44319-025-00555-w
This dataset
Open GSE288669 in finder → Find more human 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 GSE288669_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 PRJNA1218894 and SRA study SRP561376. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40835974) ↗
Study design
56 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 56 sample titles: 56 distinct titles with little repetition. 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

+ 16 more — browse all 56 samples with per-sample file links →

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.