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Integrated analysis of transcriptional and metabolic responses to mitochondrial stress

GSE241261 Homo sapiens (human) RNA-seq (gene expression) 72 samples Submitted 2025/04/14 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 72 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
Homo sapiens (human)
Samples
72 samples: 12 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
Integrated analysis of transcriptional and metabolic responses to mitochondrial stressCell reports methods · 2025
Summary (written by the submitters)
Mitochondrial stress arises from a variety of sources, including accumulation of mutations in mitochondrial DNA, generation of reactive oxygen species, and insufficient supplies of oxygen or fuel. Cells utilize multiple pathways to respond to mitochondrial injury, including mitophagy, mitochondrial fusion, and the integrated stress response / mitochondrial unfolded protein response.
Read the full summary ↓
However, the integration of transcriptional and metabolic signatures of distinct types of mitochondrial stress are still not well defined. We defined how primary human fibroblasts respond to a panel of well-characterized inhibitors that target key pathways in the mitochondria, using sub-lethal doses to trigger adaptive stress responses. By combining metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, SQUID, to infer molecular triggers of mitochondrial dysfunction in other datasets. Using SQUID, we globally investigated mitochondrial stress in the TCGA PanCancer Atlas and identified defects in pyruvate import in IDH1 mutant glioma. Altogether, these studies provide a comprehensive resource detailing cellular stress responses that safeguard mitochondrial health.
Published in
Integrated analysis of transcriptional and metabolic responses to mitochondrial stress
Kelley LP, Hu SH, Boswell SA et al. · Cell reports methods 2025 · PMID 40233762 · doi:10.1016/j.crmeth.2025.101027
This dataset
Open GSE241261 in finder → Find more human 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 GSE241261_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 PRJNA1007598 and SRA study SRP456088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40233762) ↗
Study design
12 conditions, mostly with about 6 replicates each
DMSO, ×6 UK-5099, ×6 Doxycycline, ×6 Chloramphenicol, ×6 DNP, ×6 Rotenone, ×6 Antimycin A, ×6 Metformin, ×6 +4 more

Supports a between-group comparison across 72 samples.

How we read this: 12 replicated groups read from 72 sample titles; they account for 72 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

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

Search all human 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.