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SETDB1 Orchestrates Metabolic Reprogramming to Regulate Cell State Maintenance and Cell Fate Differentiation

GSE270622 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2025/08/06 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 16 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
16 samples: 5 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
SETDB1 ensures the continuity of embryonic to adult neural stem cells through metabolic alterations in the dentate gyrusProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
In this study, we explored the function of histone methyltransferase SETDB1 in the development of the mouse dentate gyrus (DG). We discovered that a critical role of Setdb1 in steering the early development path of DG NSCs towards adult neural stem cells and astrocytes destinies.
Read the full summary ↓
In an effort to delineate the exact molecular mechanisms of aberrant postnatal NSCs and astrocytes caused by Setdb1-deleted NSCs, we utilized a suite of techniques including RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) and Setdb1-Flag Cleavage Under Targets and Tagmentation (CUT&Tag) in both wild-type (WT) and Setdb1-deficient DG samples. Combination of transcriptome and epigenome analysis indicate that COX6B2 as a key target of SETDB1 for regulating maintenance of early postnatal NSCs and differentiation of astrocytes. Taken together, our results highlight the importance of transcriptomic and chromatin landscapes for metabolic reprogramming and identify a exquisite mechanism underlyling the cell state maintenance and cell fate differentiation.
Published in
SETDB1 ensures the continuity of embryonic to adult neural stem cells through metabolic alterations in the dentate gyrus
Huang Y, Zhu Y, Zhu Y et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40699919 · doi:10.1073/pnas.2424315122
This dataset
Open GSE270622 in finder → Find more mouse 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 GSE270622_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 PRJNA1127580 and SRA study SRP515719. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40699919) ↗
Study design
5 conditions, mostly in triplicate
P7_DG_Control ×3 P7_DG_Setdb1_cKO ×3 P7_DG_ATAC_Setdb1_cKO ×3 P7_DG_ATAC_Control ×2 P7_DG_Setdb1_Flag ×2 P10_control_scRNAseq ×1 P10_Setdb1_cKO_scRNAseq ×1 P7_DG_Setdb1_Flag_Igg ×1

Supports a between-group comparison across 13 samples.

How we read this: 5 replicated groups read from 16 sample titles; they account for 13 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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