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A Role for the Transcriptional Coregulator RIP140 in the Control of Muscle Endurance Fitness [RNASeq_Training_strKO_flat]

GSE289569 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/08/27 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × EDL_muscle, Ctrl, Sedentary, vs 3 × EDL_muscle, Nrip1KO, Sedentary, vs 3 × EDL_muscle, Ctrl, Trained, vs 3 × EDL_muscle, Nrip1KO, Trained,Groups 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
A role for the transcriptional coregulator RIP140 in the control of muscle endurance fitnessJCI insight · 2025
Summary (written by the submitters)
Poor skeletal muscle fitness contributes to many chronic disease states including obesity, heart failure, primary muscle disorders, and age-related sarcopenia. Receptor Interacting Protein 140 (RIP140) is a striated muscle-enriched nuclear receptor co-regulator. To investigate the role of RIP140 in skeletal muscle, striated muscle-specific RIP140-deficient (strNrip1-/-) mice were generated and characterized.
Read the full summary ↓
strNrip1-/- mice display a remarkable endurance performance phenotype based on endurance treadmill performance, VO2max testing, and functional assessment of isolated muscle. RNA-sequence analysis of glycolytic fast-twitch muscle from the strNrip1-/- mice identified a broad array of differentially upregulated metabolic and structural muscle genes involved in muscle endurance fitness pathways including mitochondrial biogenesis and respiration, fatty acid oxidation, triglyceride dynamics, muscle fiber type, angiogenesis, and neuromuscular junction (NMJ) remodeling. Assessment of the structural correlates of these processes confirmed the function of RIP140 as placing a “brake” on the transcriptional network controlling these key muscle endurance fitness processes. Integration of the RNA sequence results with CUT&RUN analysis of strNrip1-/- myotubes identified direct RIP140 targets including genes involved in fatty acid metabolism and NMJ biogenesis. We conclude that RIP140 serves as a physiological “rheostat” for a broad network of genes involved in skeletal muscle fitness.
Published in
A role for the transcriptional coregulator RIP140 in the control of muscle endurance fitness
Pruzinsky E, Batmanov K, Medeiros DM et al. · JCI insight 2025 · PMID 41118251 · doi:10.1172/jci.insight.192376
This dataset
Open GSE289569 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 GSE289569_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 PRJNA1223460 and SRA study SRP563825. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41118251) ↗
Study design
3 × EDL_muscle, Ctrl, Sedentary, vs 3 × EDL_muscle, Nrip1KO, Sedentary, vs 3 × EDL_muscle, Ctrl, Trained, vs 3 × EDL_muscle, Nrip1KO, Trained,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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