GEO series
Mechanical regulation of the glucocorticoid-sensitive transcriptome in young and aged skeletal muscle
GSE269698
Mus musculus (mouse)
RNA-seq (gene expression)
48 samples
Submitted 2024/10/28
Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 48 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
- 48 samples: 8 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.
- Paper
- The mechanosensitive gene arrestin domain containing 2 regulates myotube diameter with direct implications for disuse atrophy with agingAmerican journal of physiology. Cell physiology · 2024
Summary (written by the submitters)
Elevated glucocorticoids alter the skeletal muscle transcriptome to induce a myopathy characterized by muscle atrophy, muscle weakness, and decreased metabolic function. These effects are more likely to occur and be more severe in aged muscle. Resistance exercise can blunt development of glucocorticoid myopathy in young muscle, but the potential to blunt the signals initiating myopathy in aged muscle is unknown.
Read the full summary ↓
To answer this, young (4-month-old) and aged (24-25-month-old) male C57BL/6 mice were randomized to receive either an intraperitoneal (IP) injection of dexamethasone (DEX; 2 mg/kg) or saline as a control. Two hours post-injections, tibialis anterior (TA) muscles of mice were subjected to unilateral high force contractions. Muscles were harvested four hours later. The glucocorticoid- and contraction-sensitive genes were determined by RNA sequencing. The number of glucocorticoid sensitive genes was similar between young and aged muscle. Contractions altered more glucocorticoid-sensitive genes in aged muscle, with this outcome primarily occurring when hormone levels were elevated. Glucocorticoid-sensitive gene programs altered by contractions were primarily related to metabolism in young mice and muscle size regulation and inflammation in aged mice. In silico analysis implied Peroxisome proliferator-activated receptor gamma-1 (PPARG) contributed to the contraction-induced changes in glucocorticoid-sensitive genes in aged muscle. Increasing PPARG expression in the TA of aged mice using Adeno-associated virus serotype 9 partially counteracted the glucocorticoid-induced reduction in Runt-related transcription factor 1 (Runx1) mRNA content, recapitulating the effects observed by contractions. Overall, these data contribute to our understanding of the mechanical regulation of the glucocorticoid transcriptome in aged skeletal muscle.
Published in
Laskin GR, Cabrera AR, Greene NP et al.
· American journal of physiology. Cell physiology 2024
· PMID 38314723
· doi:10.1152/ajpcell.00444.2023
This dataset
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.
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 GSE269698_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1123254 and SRA study SRP513554. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly with about 6 replicates each
Non-Stim TA, Young Vehicle, ×6
Stim TA, Young Vehicle, ×6
Non-Stim TA, Young DEX, ×6
Stim TA, Young DEX, ×6
Non-Stim TA, Aged Vehicle, ×6
Stim TA, Aged Vehicle, ×6
Non-Stim TA, Aged DEX, ×6
Stim TA, Aged DEX, ×6
Supports a between-group comparison across 48 samples.
How we read this: 8 replicated groups read from 48 sample titles; they account for 48 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
- GSM8324931 Non-Stim TA, Young Vehicle, 1 Non-Stim TA, Young Vehi…
- GSM8324932 Non-Stim TA, Young Vehicle, 2 Non-Stim TA, Young Vehi…
- GSM8324933 Non-Stim TA, Young Vehicle, 3 Non-Stim TA, Young Vehi…
- GSM8324934 Non-Stim TA, Young Vehicle, 4 Non-Stim TA, Young Vehi…
- GSM8324935 Non-Stim TA, Young Vehicle, 5 Non-Stim TA, Young Vehi…
- GSM8324936 Non-Stim TA, Young Vehicle, 6 Non-Stim TA, Young Vehi…
- GSM8324937 Stim TA, Young Vehicle, 1 Stim TA, Young Vehicle,
- GSM8324938 Stim TA, Young Vehicle, 2 Stim TA, Young Vehicle,
- GSM8324939 Stim TA, Young Vehicle, 3 Stim TA, Young Vehicle,
- GSM8324940 Stim TA, Young Vehicle, 4 Stim TA, Young Vehicle,
- GSM8324941 Stim TA, Young Vehicle, 5 Stim TA, Young Vehicle,
- GSM8324942 Stim TA, Young Vehicle, 6 Stim TA, Young Vehicle,
- GSM8324943 Non-Stim TA, Young DEX, 1 Non-Stim TA, Young DEX,
- GSM8324944 Non-Stim TA, Young DEX, 2 Non-Stim TA, Young DEX,
- GSM8324945 Non-Stim TA, Young DEX, 3 Non-Stim TA, Young DEX,
- GSM8324946 Non-Stim TA, Young DEX, 4 Non-Stim TA, Young DEX,
- GSM8324947 Non-Stim TA, Young DEX, 5 Non-Stim TA, Young DEX,
- GSM8324948 Non-Stim TA, Young DEX, 6 Non-Stim TA, Young DEX,
- GSM8324949 Stim TA, Young DEX, 1 Stim TA, Young DEX,
- GSM8324950 Stim TA, Young DEX, 2 Stim TA, Young DEX,
- GSM8324951 Stim TA, Young DEX, 3 Stim TA, Young DEX,
- GSM8324952 Stim TA, Young DEX, 4 Stim TA, Young DEX,
- GSM8324953 Stim TA, Young DEX, 5 Stim TA, Young DEX,
- GSM8324954 Stim TA, Young DEX, 6 Stim TA, Young DEX,
- GSM8324955 Non-Stim TA, Aged Vehicle, 1 Non-Stim TA, Aged Vehic…
- GSM8324956 Non-Stim TA, Aged Vehicle, 2 Non-Stim TA, Aged Vehic…
- GSM8324957 Non-Stim TA, Aged Vehicle, 3 Non-Stim TA, Aged Vehic…
- GSM8324958 Non-Stim TA, Aged Vehicle, 4 Non-Stim TA, Aged Vehic…
- GSM8324959 Non-Stim TA, Aged Vehicle, 5 Non-Stim TA, Aged Vehic…
- GSM8324960 Non-Stim TA, Aged Vehicle, 6 Non-Stim TA, Aged Vehic…
- GSM8324961 Stim TA, Aged Vehicle, 1 Stim TA, Aged Vehicle,
- GSM8324962 Stim TA, Aged Vehicle, 2 Stim TA, Aged Vehicle,
- GSM8324963 Stim TA, Aged Vehicle, 3 Stim TA, Aged Vehicle,
- GSM8324964 Stim TA, Aged Vehicle, 4 Stim TA, Aged Vehicle,
- GSM8324965 Stim TA, Aged Vehicle, 5 Stim TA, Aged Vehicle,
- GSM8324966 Stim TA, Aged Vehicle, 6 Stim TA, Aged Vehicle,
- GSM8324967 Non-Stim TA, Aged DEX, 1 Non-Stim TA, Aged DEX,
- GSM8324968 Non-Stim TA, Aged DEX, 2 Non-Stim TA, Aged DEX,
- GSM8324969 Non-Stim TA, Aged DEX, 3 Non-Stim TA, Aged DEX,
- GSM8324970 Non-Stim TA, Aged DEX, 4 Non-Stim TA, Aged DEX,
+ 8 more — browse all 48 samples with per-sample file links →
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Share this dataset
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.