GEO series

LSM7 Coordinates scaRNA-Mediated snRNA Modification to Ensure Spliceosome Fidelity and Spermatogonial Stem Cell Differentiation

GSE304556 Mus musculus (mouse) Single-nucleus RNA-seq 10 samples Submitted 2026/05/20 Platform GPL34290

At a glance

Single-nucleus RNA-seq · mouse · 10 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism: Mus musculus (mouse)
Samples: 10 samples: 3 × P4-testis-cKO vs 3 × P7-testis-cKO vs 2 × P4-testis-WT vs 2 × P7-testis-WTGroups 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.

Summary (written by the submitters)

Spermatogenesis requires precise spatial and temporal regulation of RNA splicing, orchestrated by both the major (U1, U2, and U4/U6/U5) and minor (U11, U12, and U4atac/U6atac/U5) spliceosomal small nuclear ribonucleoproteins (snRNPs), yet their function during germ cell development remain poorly defined. Here, we elucidate the essential function of LSM7, a component of the LSM2-8 complex, in snRNP biogenesis and the process of spermatogenesis.

Read the full summary ↓

Our results demonstrate that LSM7 governs the stability of U6 small nuclear RNA (snRNA) within Cajal bodies and directly interacts with scaRNA2, scaRNA13, and scaRNA17 to modulate 2′-O-methylation (2′-O-Me) and pseudouridylation (Ψ) modifications of U2 and U12 snRNAs. Loss of LSM7 results in defective nuclear localization and reduced stability of U6, U2, U5, and U12 snRNAs, destabilization of their corresponding snRNP complexes, and aberrant splicing events, notably affecting mutually exclusive exons (MXE) and exon skipping (SE). These splicing defects lead to translational dysregulation, ultimately impairing the differentiation of spermatogonial stem cells (SSCs) into spermatogonia. Our findings identify LSM7 as a pivotal regulator linking scaRNA-guided snRNA modifications, spliceosomal fidelity, and the determination of spermatogonial stem cell fate, offering important mechanistic insights into the post-transcriptional regulation of male germ cell development.

This dataset

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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 GSE304556_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1301787 and SRA study SRP606760. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × P4-testis-cKO vs 3 × P7-testis-cKO vs 2 × P4-testis-WT vs 2 × P7-testis-WT

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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

GSM9152815 P4-testis-WT1 P4-testis-WT
GSM9152816 P4-testis-WT2 P4-testis-WT
GSM9152817 P4-testis-cKO1 P4-testis-cKO
GSM9152818 P4-testis-cKO2 P4-testis-cKO
GSM9152819 P4-testis-cKO3 P4-testis-cKO
GSM9152820 P7-testis-WT1 P7-testis-WT
GSM9152821 P7-testis-WT2 P7-testis-WT
GSM9152822 P7-testis-cKO1 P7-testis-cKO
GSM9152823 P7-testis-cKO2 P7-testis-cKO
GSM9152824 P7-testis-cKO3 P7-testis-cKO

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