GEO series

Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance (bulk RNA-Seq)

GSE267909 Mus musculus (mouse) Single-nucleus RNA-seq 14 samples Submitted 2025/02/10 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 14 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). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 14 samples: 4 × AAV_control vs 4 × AAV_Pdzrn4_OE vs 3 × AAV_Etv4_OE vs 3 × AAV_Lrtm1_OEGroups 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: Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenanceNature communications · 2025

Summary (written by the submitters)

The neuromuscular junction (NMJ) is the synapse formed between motor neurons and skeletal muscle fibers. Its stability relies on the continued expression of genes in a subset of myonuclei, called NMJ myonuclei. Here, we use single-nuclei RNA-sequencing (snRNA-seq) to identify numerous undescribed NMJ-specific transcripts. To elucidate how the NMJ transcriptome is regulated, we also performed snRNA-seq on sciatic nerve transected, botulinum toxin injected and Musk knockout muscles.

Read the full summary ↓

These data show that NMJ gene expression is not only driven by agrin-Lrp4/MuSK signaling, but is also affected by electrical activity and trophic factors other than agrin. By selecting three previously undescribed NMJ genes Etv4, Lrtm1 and Pdzrn4, we further characterize novel contributors to NMJ stability and function. AAV-mediated overexpression and AAV-CRISPR/Cas9-mediated knockout show that Etv4 is sufficient to upregulate expression of ~50% of the NMJ genes in non-synaptic myonuclei, while muscle-specific knockout of Pdzrn4 induces NMJ fragmentation. Further investigation of Pdzrn4 revealed that it localizes to the Golgi apparatus and interacts with MuSK protein. Collectively, our data provide a rich resource of NMJ transcripts, highlight the importance of ETS transcription factors at the NMJ and suggest a novel pathway for NMJ post-translational modifications.

Published in

Single-nuclei sequencing of skeletal muscle reveals subsynaptic-specific transcripts involved in neuromuscular junction maintenance

Ham AS, Lin S, Tse A et al. · Nature communications 2025 · PMID 40044687 · doi:10.1038/s41467-025-57487-1

This dataset

Open GSE267909 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 GSE267909_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 PRJNA1113626 and SRA study SRP508817. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40044687) ↗

Study design

4 × AAV_control vs 4 × AAV_Pdzrn4_OE vs 3 × AAV_Etv4_OE vs 3 × AAV_Lrtm1_OE

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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

GSM8281456 AAV_control_1 AAV_control
GSM8281457 AAV_control_2 AAV_control
GSM8281458 AAV_control_3 AAV_control
GSM8281459 AAV_control_4 AAV_control
GSM8281460 AAV_Etv4_OE_1 AAV_Etv4_OE
GSM8281461 AAV_Etv4_OE_2 AAV_Etv4_OE
GSM8281462 AAV_Etv4_OE_3 AAV_Etv4_OE
GSM8281463 AAV_Lrtm1_OE_1 AAV_Lrtm1_OE
GSM8281464 AAV_Lrtm1_OE_2 AAV_Lrtm1_OE
GSM8281465 AAV_Lrtm1_OE_3 AAV_Lrtm1_OE
GSM8281466 AAV_Pdzrn4_OE_1 AAV_Pdzrn4_OE
GSM8281467 AAV_Pdzrn4_OE_2 AAV_Pdzrn4_OE
GSM8281468 AAV_Pdzrn4_OE_3 AAV_Pdzrn4_OE
GSM8281469 AAV_Pdzrn4_OE_4 AAV_Pdzrn4_OE

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