← BioTransfer GEO Dataset Finder
GEO series

Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [ATAC-Seq]

GSE266172 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 31 samples Submitted 2025/04/29 Platform GPL34290Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 31 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
31 samples: 8 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
Sex-specific expression and function of TRIM28 during mouse primordial germ differentiationiScience · 2025
Summary (written by the submitters)
Transposable elements are increasingly appreciated as regulatory elements in early mammalian development, especially in cells which exhibit pluripotency. Mammalian primordial germ cells (PGCs) must exit latent pluripotency in a process termed determination before they are competent to differentiate and enter sex-specific developmental programs.
Read the full summary ↓
Here, we find that determination is marked by large changes to the transposable element (TE) repertoire, a phenomenon driven by TRIM28, after which testicular and ovarian PGCs exhibit district transposable element repertoires. We find that loss of TRIM28 perturbs entry into determination as marked by expression of DAZL in a sex-specific manner, but does not result in a failure to downregulate markers of latent pluripotency, including SOX2 and NANOG in either sex. Despite downregulation of some early PGC markers, both ovarian and testicular PGCs fail to properly enter into their meiotic germ cell or prospermatogonial programs, respectively. Thus, we show that TRIM28-mediated reorganization of the TE repertoire is necessary to establish a PGC epigenome competent for proper germline commitment and gametogenesis.
Published in
Sex-specific expression and function of TRIM28 during mouse primordial germ differentiation
DiRusso JA, Zhan L, Tao Y et al. · iScience 2025 · PMID 41019377 · doi:10.1016/j.isci.2025.113474
This dataset
Open GSE266172 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 GSE266172_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 PRJNA1106060 and SRA study SRP504776. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41019377) ↗
Study design
8 conditions, mostly with about 4 replicates each
E10.5_PGC_Male_TRIM28KO_ATAC ×5 E10.5_PGC_Male_Control_ATAC ×4 E10.5_PGC_Female_Control_ATAC ×4 E10.5_PGC_Female_TRIM28KO_ATAC ×4 E14.5_PGC_Male_Control_ATAC ×4 E14.5_PGC_Female_Control_ATAC ×4 E14.5_PGC_Male_TRIM28_ATAC ×3 E14.5_PGC_Female_TRIM28_ATAC ×3

Supports a between-group comparison across 31 samples.

How we read this: 8 replicated groups read from 31 sample titles; they account for 31 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

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.