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

GSE266176 Mus musculus (mouse) RNA-seq (gene expression) 42 samples Submitted 2025/04/29 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 42 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
42 samples: 12 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 GSE266176 in finder → Find more mouse RNA-seq 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 GSE266176_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1106064 and SRA study SRP504772. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41019377) ↗
Study design
12 conditions, mostly with about 4 replicates each
E11.5_PGC_Control_Male ×4 E11.5_PGC_TRIM28KO_Male ×4 E12.5_PGC_Control_Male ×4 E12.5_PGC_Control_Female ×4 E12.5_PGC_TRIM28KO_Female ×4 E13.5_PGC_TRIM28KO_Male ×4 E11.5_PGC_Control_Female ×3 E11.5_PGC_TRIM28KO_Female ×3 +4 more

Supports a between-group comparison across 42 samples.

How we read this: 12 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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