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The nuclear interactome of 14-3-3zeta reveals its critical roles for genome accessibility during early stages of adipogenesis

GSE262016 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/08/18 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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
14-3-3ζ allows for adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiationMolecular metabolism · 2025
Summary (written by the submitters)
Little is known about the molecular factors that tightly coordinate sequential actions of adipogenic cellular pathways that occur during the early stages of adipocyte precursor cells (APCs) differentiation. We previously established the scaffold protein, 14-3-3ζ, as a critical regulator of adipogenesis (Lim et al., Nat Commun., 2015).
Read the full summary ↓
Our proteomic analysis performed in the present study suggested functional interactions between 14-3-3ζ and epigenetic effectors, such as DNMTs and HDACs, during the intial stages of APC differentiation. To assess if or how 14-3-3ζ influences chromatin accessibility in differentiating APCs, we performed ATAC-seq on 3T3-L1 preadipocytes that were transfected with a control, non-targeting siRNA (siCon) or siRNA against Ywhaz (sizeta), the gene encoding 14-3-3ζ (using either a Ywhaz-targeting or a control siRNA), followed by differentiation with the adipogenic cocktail (MDI) for 0h, 24h and 48h. Our ATAC-seq analysis revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial 48 hours of differentiation. In conclusion, we report 14-3-3ζ as a key epigenetic modulator during induction of adipogenesis.
Published in
14-3-3ζ allows for adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation
Rial SA, You Z, Vivoli A et al. · Molecular metabolism 2025 · PMID 40306359 · doi:10.1016/j.molmet.2025.102159
This dataset
Open GSE262016 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 GSE262016_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 PRJNA1090046 and SRA study SRP496679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40306359) ↗
Study design
6 conditions, mostly with about 4 replicates each
3T3-L1, siCon, -MDI, ×4 3T3-L1, siYwhaz, -MDI, ×4 3T3-L1, siCon, +24 hr MDI, ×4 3T3-L1, siYwhaz, +24 hr MDI, ×4 3T3-L1, siCon, +48 hr MDI, ×4 3T3-L1, siYwhaz, +48 hr MDI, ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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