GEO series

CUX1 Manifests Species-Dependent Regulation in Controlling Adipocyte Differentiation [ChIP-Seq]

GSE293544 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 6 samples Submitted 2026/04/02 Platform GPL16791Platform GPL17021

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 6 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: 6 samples: 6 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 transcription factor CUX1 exerts opposing roles in human and mouse adipocyte differentiationMolecular metabolism · 2026

Summary (written by the submitters)

Adipocyte differentiation, also known as adipogenesis, is a crucial process for maintaining the adipocyte pool and plays a key role in insulin sensitivity and systemic metabolism. Adipogenesis is governed by master transcription factors, such as C/EBPβ. However, there remains an unmet need to identify novel transcriptional factors within the C/EBPβ regulatory network in the differentiation of primary human adipose-derived precursor cells (hAPCs).

Read the full summary ↓

Chromatin immunoprecipitation and selective isolation of chromatin-associated proteins (ChIP-SICAP) and CRISPR/cas9 knockout (KO) screening approach was applied in hAPCs. RNA-seq and ChIP-seq were also utilized for pathway and gene enrichment analyses. We also constructed a APCs-specific KO mouse model. Deletion of CUX1 in hAPCs impairs adipogenesis, whereas CUX1 overexpression (OE) increases human adipogenesis. RNA-seq and ChIP-seq analyses reveal that CUX1 promotes the expression of key adipogenic genes, including PPARG, a master regulator of adipocyte fate determination. Interestingly, Cux1 deletion enhances, while CUX1-OE suppresses adipogenesis in mouse APCs (mAPCs). ChIP-seq analysis of CUX1 in mAPCs further supports its contrasting role in mice. Additionally, in vivo tracing of mAPCs shows that Cux1 deletion promotes adipocyte differentiation. Collectively, these findings highlight that CUX1 exerts species-specific regulation of adipogenesis, acting as a differential regulator of fat development in humans and mice.

Published in

The transcription factor CUX1 exerts opposing roles in human and mouse adipocyte differentiation

Chen Y, Liu L, Calhoun RP et al. · Molecular metabolism 2026 · PMID 41318063 · doi:10.1016/j.molmet.2025.102290

This dataset

Open GSE293544 in finder → Find more 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 GSE293544_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 PRJNA1245158 and SRA study SRP575902. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41318063) ↗

Study design

6 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 2 samples read as cases, 2 as controls.

How we read this: Read from 6 sample titles: 6 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

GSM8884921 Human, adipose-derived precursor cells, CUX1 Control
GSM8884922 Human, adipose-derived precursor cells, CUX1 Knockout
GSM8884923 Human, adipose-derived precursor cells, input
GSM8884924 Mouse, adipose-derived precursor cells, Cux1 Control
GSM8884925 Mouse, adipose-derived precursor cells, Cux1 Knockout
GSM8884926 Mouse, adipose-derived precursor cells, input

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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.