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Multi-organ Transcriptome Atlas of a Mouse Model of Relative Energy Deficiency in Sport (REDs)

GSE243060 Mus musculus (mouse) RNA-seq (gene expression) 419 samples Submitted 2024/08/07 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 419 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
419 samples: 134 conditions, mostly in triplicateGroups 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-organ transcriptome atlas of a mouse model of relative energy deficiency in sportCell metabolism · 2024
Summary (written by the submitters)
Insufficient energy intake to meet energy expenditure demands of physical activity can result in systemic neuroendocrine and metabolic abnormalities in activity-dependent anorexia and Relative Energy Deficiency in Sport (REDs). REDs affects >40% of athletes, yet the lack of underlying molecular changes has been a hurdle to have a better understanding of REDs and its treatment.
Read the full summary ↓
To assess the molecular changes in response to energy deficiency, we implemented the ‘exercise-for-food’ paradigm, in which, food reward size is determined by wheel-running activity. By using this paradigm, we replicated several aspects of REDs in female and male mice, with high physical activity, and gradually reduced food intake, which results in weight loss, compromised bone health, organ-specific mass changes and altered rest-activity patterns. By integrating transcriptomics of 19 different organs, we provide a comprehensive dataset that will guide future understanding of REDs and may provide important implications for metabolic health and (athletic) performance.
Published in
Multi-organ transcriptome atlas of a mouse model of relative energy deficiency in sport
van Rosmalen L, Zhu J, Maier G et al. · Cell metabolism 2024 · PMID 39232281 · doi:10.1016/j.cmet.2024.08.001
This dataset
Open GSE243060 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 GSE243060_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 PRJNA1015634 and SRA study SRP459928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39232281) ↗
Study design
134 conditions, mostly in triplicate
Pituitary, female, Control, ZT05, ×3 Pituitary, female, Control, ZT17, ×3 Pituitary, female, Deficient, ZT05, ×3 Pituitary, female, Deficient, ZT17, ×3 Pituitary, male, Control, ZT05, ×3 Pituitary, male, Control, ZT17, ×3 Pituitary, male, Deficient, ZT05, ×3 Pituitary, male, Deficient, ZT17, ×3 +126 more

Supports a between-group comparison across 400 samples.

How we read this: 134 replicated groups read from the first 400 of 419 sample titles; they account for 400 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

+ 379 more — browse all 419 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.