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Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy: longread sequencing of Clcn1 transcripts in muscle from Mbnl1 knockout, Exon 7a deletion, and ADR mice.

GSE311013 Mus musculus (mouse) RNA-seq (gene expression) 27 samples Submitted 2026/04/27 Platform GPL24198
At a glance

RNA-seq (gene expression) · mouse · 27 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
27 samples: 9 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.
Summary (written by the submitters)
A cardinal sign of myotonic dystrophy type 1 (DM1) is myotonia, slow muscle relaxation after voluntary contraction. Myotonia results from mis-regulated splicing of chloride channel 1 (ClC-1), leading to loss of channel function and runs of involuntary action potentials in muscle fibers. Heralding the onset of weakness, myotonia is often the first symptom of DM1, and thus this raises the possibility that muscle hyperexcitability promotes the subsequent development of myopathy.
Read the full summary ↓
We used genome editing to test this possibility by deleting the alternatively spliced and frameshift inducing ClC-1 exon 7a (E7a) in the Mbnl1 knockout model of DM1. Although several ClC-1 exons exhibit mis-regulated splicing in DM1, deletion of this single cryptic exon was sufficient to restore ClC-1 function and eliminate myotonia systemically and permanently. We utilized long-read sequencing to assess transcript isoform utilization in mice with Mbnl1 knockout, deletion of E7a reduced the frequency of other splicing defects in ClC-1 transcripts, likely as a passive consequence of restoring reading frame and nonsense surveillance.
This dataset
Open GSE311013 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 GSE311013_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 PRJNA1368488 and SRA study SRP647928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
WT mouse, P7, Quad tissue, Clcn1 amp from E1-… ×3 Clcn1 delta E7a mouse, P7, Quad tissue, Clcn1… ×3 Mbnl1 knockout mouse, P7, Quad tissue, Clcn1 … ×3 Mbnl1 knockout; Clcn1 delta E7a mouse, P7, Qu… ×3 WT mouse, P18, Quad tissue, Clcn1 amp from E1… ×3 Clcn1 delta E7a mouse, P18, Quad tissue, Clcn… ×3 Mbnl1 knockout mouse, P18, Quad tissue, Clcn1… ×3 Mbnl1 knockout; Clcn1 delta E7a mouse, P18, Q… ×3 +1 more

Supports a case/control comparison: 12 samples read as cases, 6 as controls.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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
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