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PRDM16 functions as a co-repressor in the BMP pathway to suppress neural stem cell proliferation

GSE275758 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 86 samples Submitted 2025/04/24 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 86 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
86 samples: 22 conditions, mostly in triplicateGroups 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
PRDM16 functions as a co-repressor in the BMP pathway to suppress neural stem cell proliferationeLife · 2025
Summary (written by the submitters)
BMP signalling acts as an instructive cue in various developmental processes such as tissue patterning, stem cell proliferation, and differentiation. However, it is not fully understood how this signalling pathway generates different cell-specific outputs. Here we have identified PRDM16 as a key co-factor for BMP signalling. PRDM16 contributes to a repressive role of BMP signalling on neural stem cell (NSC) proliferation.
Read the full summary ↓
We demonstrate that PRDM16 regulates the genomic distribution of BMP pathway transcription factors, the SMAD4/pSMAD complex, preventing the activation of cell proliferation genes. When Prdm16 is lost, the SMAD complex relocates to nearby genomic regions, leading to abnormal upregulation of BMP target genes. This function of PRDM16 is also required for the specification of choroid plexus (ChP) epithelial cells. Through a single-cell resolution fluorescent in situ approach, we have observed that genes co-repressed by SMAD and PRDM16, such as Wnt7b and several cell cycle regulators, become overexpressed in Prdm16 mutant ChP. Our findings elucidate a mechanism through which SMAD4 and pSMAD1/5/8 repress gene expression. Moreover, our study suggests a regulatory circuit composed of BMP and Wnt signaling, along with PRDM16, in controlling stem cell behaviors.
Published in
PRDM16 functions as a co-repressor in the BMP pathway to suppress neural stem cell proliferation
He L, Wen J, Dai Q · eLife 2025 · PMID 40658097 · doi:10.7554/eLife.104076
This dataset
Open GSE275758 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 GSE275758_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 PRJNA1152921 and SRA study SRP528877. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40658097) ↗
Study design
22 conditions, mostly in triplicate
Prdm16NSC_Input ×3 Prdm16NSC_pSMAD ×3 Prdm16NSC_SMAD3 ×3 Prdm16NSC_SMAD4 ×3 Prdm16NSC_BMP4_Input ×3 Prdm16NSC_BMP4_pSMAD ×3 Prdm16NSC_BMP4_SMAD3 ×3 Prdm16NSC_BMP4_SMAD4 ×3 +35 more

Supports a case/control comparison: 33 samples read as cases, 6 as controls.

How we read this: 22 replicated groups read from 86 sample titles; they account for 65 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

+ 46 more — browse all 86 samples with per-sample file links →

Datasets on a similar topic

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