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Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [circadian RNA-seq]

GSE273878 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2025/05/11 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: 18 conditions, mostly in duplicateGroups 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
Cancer-induced FOXP1 disrupts and reprograms skeletal-muscle circadian transcription in cachexiaCell reports · 2025
Summary (written by the submitters)
Cancer cachexia is a debilitating metabolic disorder characterized by involuntary loss of body and muscle mass, leading to increased morbidity and mortality. We previously found that Forkhead box P1 (FoxP1) upregulation in skeletal muscle causes muscle wasting and is required for muscle wasting in response to cancer. However, transcriptional networks targeted by FoxP1 in skeletal muscles undergoing cancer-induced wasting remain largely unknown.
Read the full summary ↓
Here, we identify FoxP1 as a key disruptor of the skeletal muscle clock in response to cancer, that reprograms circadian patterns of gene expression at cachexia onset. Specifically, we show that cancer-induced FoxP1 rewires the skeletal muscle circadian transcriptome towards pathways associated with muscle wasting and disrupts the temporal patterning of pathways governing glucose, lipid, and oxidative metabolism. These findings thus implicate cancer/disease-specific functions of FOXP1 in the disruption and reprograming of the skeletal muscle circadian transcriptome which may contribute to muscle wasting and the development of cachexia.
Published in
Cancer-induced FOXP1 disrupts and reprograms skeletal-muscle circadian transcription in cachexia
Ducharme JB, Neyroud D, Schonk MM et al. · Cell reports 2025 · PMID 40349340 · doi:10.1016/j.celrep.2025.115689
This dataset
Open GSE273878 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 GSE273878_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 PRJNA1143531 and SRA study SRP523955. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40349340) ↗
Study design
18 conditions, mostly in duplicate
00/circadian time 18, ×4 00/circadian time 22, ×4 00/circadian time 26, ×4 00/circadian time 30, ×4 00/circadian time 34, ×4 00/circadian time 38, ×4 Muscle, sham/control, FoxP1 skeletal muscle K… ×2 Muscle, sham/control, FoxP1 skeletal muscle K… ×2 +10 more

Supports a between-group comparison across 48 samples.

How we read this: 18 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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