GEO series

Nodal/Smad2 signaling sustains developmental pausing by repressing Pparg -mediated lipid metabolism [ATAC-seq]

GSE302996 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2026/06/22 Platform GPL34328

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.

Summary (written by the submitters)

Cells and organisms can enter transient dormant states to survive unfavorable conditions during development, physiological adult states and disease. One paradigmatic case of dormancy is diapause, whereby embryos transiently pause development and enter a state of suspended animation. In mammals, diapause occurs pre-implantation at the blastocyst state and involves global growth suppression and metabolic rewiring towards lipid usage as energy source.

Read the full summary ↓

The molecular regulation of diapause remains poorly understood, including whether it occurs by default or requires active signaling. Here, we identify the canonical TGF-β signaling pathway as an essential driver of transcriptional and metabolic reprogramming in diapause. TGF-β signaling was thought to only be required post-implantation, but we show that the ligand Nodal and its downstream effector Smad2 are essential for the survival of paused embryonic stem cells (ESCs) and blastocysts. Mechanistically, we found that Smad2 represses a Pparg, a transcription factor that is a master regulator of lipid storage, a process incompatible with pausing. Ablation of Pparg in Smad2-deficient ESCs rescues their survival and prevents excess lipid buildup in pausing conditions. These findings establish Nodal/Smad2 signaling as pivotal for sustaining embryonic diapause and suggest that the crosstalk between TGF-β signaling and the Pparg pathway may be broadly relevant for metabolic rewiring in dormancy contexts.

This dataset

Open GSE302996 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 GSE302996_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 PRJNA1293325 and SRA study SRP601770. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

ATAC, Ctrl, WT, ×4 ATAC, Ctrl, Smad2_KO1, ×4 ATAC, Ctrl, Smad2_KO2, ×4 ATAC, Paused, WT, ×4 ATAC, Paused, Smad2_KO1, ×4 ATAC, Paused, Smad2_KO2, ×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

GSM9115326 ATAC, Ctrl, WT, rep 1 ATAC, Ctrl, WT,
GSM9115327 ATAC, Ctrl, WT, rep 2 ATAC, Ctrl, WT,
GSM9115328 ATAC, Ctrl, WT, rep 3 ATAC, Ctrl, WT,
GSM9115329 ATAC, Ctrl, WT, rep 4 ATAC, Ctrl, WT,
GSM9115330 ATAC, Ctrl, Smad2_KO1, rep 1 ATAC, Ctrl, Smad2_KO1,
GSM9115331 ATAC, Ctrl, Smad2_KO1, rep 2 ATAC, Ctrl, Smad2_KO1,
GSM9115332 ATAC, Ctrl, Smad2_KO1, rep 3 ATAC, Ctrl, Smad2_KO1,
GSM9115333 ATAC, Ctrl, Smad2_KO1, rep 4 ATAC, Ctrl, Smad2_KO1,
GSM9115334 ATAC, Ctrl, Smad2_KO2, rep 1 ATAC, Ctrl, Smad2_KO2,
GSM9115335 ATAC, Ctrl, Smad2_KO2, rep 2 ATAC, Ctrl, Smad2_KO2,
GSM9115336 ATAC, Ctrl, Smad2_KO2, rep 3 ATAC, Ctrl, Smad2_KO2,
GSM9115337 ATAC, Ctrl, Smad2_KO2, rep 4 ATAC, Ctrl, Smad2_KO2,
GSM9115338 ATAC, Paused, WT, rep 1 ATAC, Paused, WT,
GSM9115339 ATAC, Paused, WT, rep 2 ATAC, Paused, WT,
GSM9115340 ATAC, Paused, WT, rep 3 ATAC, Paused, WT,
GSM9115341 ATAC, Paused, WT, rep 4 ATAC, Paused, WT,
GSM9115342 ATAC, Paused, Smad2_KO1, rep 1 ATAC, Paused, Smad2_KO1,
GSM9115343 ATAC, Paused, Smad2_KO1, rep 2 ATAC, Paused, Smad2_KO1,
GSM9115344 ATAC, Paused, Smad2_KO1, rep 3 ATAC, Paused, Smad2_KO1,
GSM9115345 ATAC, Paused, Smad2_KO1, rep 4 ATAC, Paused, Smad2_KO1,
GSM9115346 ATAC, Paused, Smad2_KO2, rep 1 ATAC, Paused, Smad2_KO2,
GSM9115347 ATAC, Paused, Smad2_KO2, rep 2 ATAC, Paused, Smad2_KO2,
GSM9115348 ATAC, Paused, Smad2_KO2, rep 3 ATAC, Paused, Smad2_KO2,
GSM9115349 ATAC, Paused, Smad2_KO2, rep 4 ATAC, Paused, Smad2_KO2,

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