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Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis [RNA-Seq]

GSE281948 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/12/25 Platform GPL21273Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 7 × GFRa1+/Kit-, cryptorchid RNA, vs 5 × GFRa1+/Kit-, control RNA,Groups 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
Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testisDevelopment (Cambridge, England) · 2025
Summary (written by the submitters)
Cryptorchidism is the most frequent congenital defect in newborn males characterized by the absence of the testis from the scrotum. Approximately 90% of patients with untreated bilateral cryptorchidism exhibit azoospermia due to defective spermatogenesis in the affected testis. While abnormal spermatogonial stem cell maintenance or differentiation is suggested to cause germ cell degeneration in the cryptorchid testis, underlying molecular mechanisms remain unclear.
Read the full summary ↓
Here we profiled spermatogonial epigenetic landscapes using surgically induced cryptorchid testis in the mouse. We show that cryptorchidism leads to alterations in local, but not global H3K27me3 and H3K9me3 in undifferentiated spermatogonia. Of these, the loss of H3K27me3 leads to activation of developmental and apoptotic pathway genes that are repressed by the polycomb machineries in germ cells. Cryptorchid spermatogonia exhibit the increase of H3K27me3 demethylases KDM6A and KMD6B. Furthermore, we reveal that an increased temperature leads to Kdm6a/b upregulation in germline stem cells cultured in vitro. Thus, our study suggests that a temperature-dependent histone demethylation induces mRNA dysregulation due to the partial loss of H3K27me3 in spermatogonia.
Published in
Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis
Kuroha K, Dočkal I, Radović U et al. · Development (Cambridge, England) 2025 · PMID 39745222 · doi:10.1242/dev.204239
This dataset
Open GSE281948 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 GSE281948_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 PRJNA1186236 and SRA study SRP545317. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39745222) ↗
Study design
7 × GFRa1+/Kit-, cryptorchid RNA, vs 5 × GFRa1+/Kit-, control RNA,

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 12 sample titles; they account for 12 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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