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Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesis

GSE196779 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2026/02/11 Platform GPL28330
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 12 conditions, mostly in triplicateGroups 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
Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesisNature communications · 2026
Summary (written by the submitters)
During spermatogenesis, the unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI) and form a heterochromatic XY body. Defects in MSCI lead to meiotic arrest and male infertility. Although DNA damage response (DDR) factors are established as key initiators of MSCI, how transcriptional silencing is subsequently achieved remains elusive.
Read the full summary ↓
Here, we identify the nucleolar components NPM1, SENP3, and rRNA as essential downstream effectors of DDR signaling in MSCI. During pachytene, these components migrate to and transiently cover the XY body during MSCI establishment, before becoming restricted to a corner of the XY body. Genetic deletion of Npm1 or Senp3, or inhibition of rRNA transcription severely impairs MSCI. Mechanistically, SENP3-mediated deSUMOylation of NPM1 promotes its interaction with rRNA, enabling liquid-liquid phase separation, via which they exclude Pol II from the XY body. Together, these data reveal a previously unrecognized role of nucleolar components in the transcriptional regulation of MSCI in mammalian spermatogenesis.
Published in
Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesis
Li M, Du Z, Li H et al. · Nature communications 2026 · PMID 41888129 · doi:10.1038/s41467-026-70932-z
This dataset
Open GSE196779 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 GSE196779_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 PRJNA807299 and SRA study SRP359944. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41888129) ↗
Study design
12 conditions, mostly in triplicate
spermatocytes, pachytene, Senp3-control, ×3 spermatocytes, pachytene, Senp3-SKO, ×3 spermatocytes, pachytene, Npm1-control, ×3 spermatocytes, pachytene, Npm1-SKO, ×3 spermatocytes, pachytene, Npm1-control2, ×3 spermatocytes, pachytene, Npm1-CKI, ×3 spermatocytes, pachytene, DMSO, ×2 spermatocytes, pachytene, AZD6738, ×2 +4 more

Supports a between-group comparison across 30 samples.

How we read this: 12 replicated groups read from 30 sample titles; they account for 30 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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