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Transcriptomic profiling of mouse aging soleus muscles and drug interventions

GSE338580 Mus musculus (mouse) RNA-seq (gene expression) 78 samples Submitted 2026/08/04 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 78 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
78 samples: 9 conditions, mostly with about 6 replicates eachGroups 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)
Here, we performed bulk RNA sequencing on soleus muscles of both male and female mice at four different life stages (6, 12, 20, and 28 months). We showed that aging soleus muscle mice follows and shift on gene expression pattern during aging. Network analysis showed that modules enriched in mitochondria showed a down-then-up trend during aging, resembles the expression pattern of longevity-associated modules in C.elegans.
Read the full summary ↓
We also associated expression of conserved module with frailty and found that the expression of the mitochondria/ribosome module is positively associated with frailty at 28 months in male mice. In addition, we treated mice with four different compounds from 20 months to 28 months, recorded their frailty change over time and performed RNA-seq on their soleus muscles. We found that aKG treatment in male mice significantly reduced frailty index and exhibted an decrease in expression of mitochondria/ribosome modules. Together, we represent a large transcriptomic cohort of aging and drug interventions on mouse soleus muscles. Our study showed the sex-specific beneficial effects on compounds that identified conserved co-expression modules during aging that are associated with longevity.
This dataset
Open GSE338580 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 GSE338580_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 PRJNA1495203 and SRA study SRP717915. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly with about 6 replicates each
Control M28 M, ×15 Control M28 F, ×13 CaAKG M28 M, ×12 Control Mo20 M, replciate ×9 Control Mo12 F, replcate ×7 Control Mo12 M, replcate ×6 Control Mo20 F, ×6 Control Mo6 M, ×6 +1 more

Supports a between-group comparison across 78 samples.

How we read this: 9 replicated groups read from 78 sample titles; they account for 78 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

+ 38 more — browse all 78 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.