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Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation [CUT&Tag]

GSE306920 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2026/02/12 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
22 samples: 11 conditions, mostly in duplicateGroups 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
Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for ActivationResearch square · 2025
Summary (written by the submitters)
Female mammals are born with a finite pool of non-growing oocytes (NGOs) housed in primordial follicles, forming the ovarian reserve that determines reproductive lifespan. Mechanisms underlying the reserve’s long-term maintenance and subsequent follicular activation remain elusive. Using total RNA sequencing and de novo transcriptome assembly across perinatal oogenesis in mice, we captured the full oocyte transcriptome.
Read the full summary ↓
We show that NGOs establish extensive accessible chromatin at gene regulatory elements—including promoters and enhancers—with formation of many regions driven by newly evolved endogenous retroviruses. In NGOs, epigenetic priming for follicular activation involves pre-loading RNA polymerase II and transcription factors TCF3 and TCF12 at these sites, counteracted by repression via Polycomb Repressive Complex 1-mediated H2AK119 ubiquitylation. This transposable element (TE)-mediated epigenetic priming underlies the ovarian reserve’s long-term maintenance and poises oocytes for activation. Our findings establish the ovarian reserve as an actively primed population, with newly evolved TEs orchestrating genome-wide transcriptional activation.
Published in
Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation
Munakata Y, Hu M, Dani R et al. · Research square 2025 · PMID 41377959 · doi:10.21203/rs.3.rs-8081066/v1
This dataset
Open GSE306920 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 GSE306920_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 PRJNA1313917 and SRA study SRP616257. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41377959) ↗
Study design
11 conditions, mostly in duplicate
WT_CT_NGO_TCF3 ×2 WT_CT_NGO_TCF12 ×2 WT_CT_E18O_Total-PolII ×2 WT_CT_NGO_Total-PolII ×2 WT_CT_GO_Total-PolII ×2 WT_CT_E18O_S2P-PolII ×2 WT_CT_NGO_S2P-PolII ×2 WT_CT_GO_S2P-PolII ×2 +3 more

Supports a between-group comparison across 22 samples.

How we read this: 11 replicated groups read from 22 sample titles; they account for 22 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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