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Multi-omics profiling of cachexia-targeted tissues reveals a spatio-temporally coordinated response to cancer

GSE290937 Mus musculus (mouse) RNA-seq (gene expression) 80 samples Submitted 2025/11/05 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 80 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
80 samples: 20 conditions, mostly with about 4 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
Multi-omics profiling of cachexia-targeted tissues reveals a spatio-temporally coordinated response to cancerNature metabolism · 2026
Summary (written by the submitters)
Cachexia is a wasting disorder associated with high morbidity and mortality in patients with cancer. Tumour-host interaction and maladaptive metabolic reprogramming are substantial, yet poorly understood, contributors to cachexia. Here we present a comprehensive overview of the spatio-temporal metabolic reprogramming during cachexia, using integrated metabolomics, RNA sequencing and 13C-glucose tracing data from multiple tissues and tumours of C26 tumour-bearing male mice at different disease stages.
Read the full summary ↓
We identified one-carbon metabolism as a tissue-overarching pathway characteristic for metabolic wasting in mice and patients and linked to inflammation, glucose hypermetabolism and atrophy in muscle. The same metabolic rewiring also occurred in five additional mouse models, namely Panc02, 8025, ApcMin, LLC and KPP, and a humanised cachexia mouse model. Together, our study provides a molecular framework for understanding metabolic reprogramming and the multi-tissue metabolite-coordinated response during cancer cachexia progression, with one-carbon metabolism as a tissue-overarching mechanism linked to wasting.
Published in
Multi-omics profiling of cachexia-targeted tissues reveals a spatio-temporally coordinated response to cancer
Morigny P, Vondrackova M, Ji H et al. · Nature metabolism 2026 · PMID 41540255 · doi:10.1038/s42255-025-01434-3
This dataset
Open GSE290937 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 GSE290937_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 PRJNA1231033 and SRA study SRP567610. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41540255) ↗
Study design
20 conditions, mostly with about 4 replicates each
Pre-cachectic tumor mouse, Liver, Mouse # ×4 Pre-cachectic tumor mouse, Inguinal adipose t… ×4 Pre-cachectic tumor mouse, Heart, Mouse # ×4 Pre-cachectic tumor mouse, GC muscle, Mouse # ×4 Pre-cachectic tumor mouse, Epididymal adipose… ×4 Healthy control mouse (PBS-injected), Liver, … ×4 Healthy control mouse (PBS-injected), Inguina… ×4 Healthy control mouse (PBS-injected), Heart, … ×4 +12 more

Supports a case/control comparison: 60 samples read as cases, 20 as controls.

How we read this: 20 replicated groups read from 80 sample titles; they account for 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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