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Transcriptomic analyses of mouse livers from an 18-month oral carcinogenicity study of HFPO-DA with a 9-month chronic toxicity phase

GSE250389 Mus musculus (mouse) RNA-seq (gene expression) 92 samples Submitted 2025/12/29 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 92 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
92 samples: 92 samples, each with a distinct title — no replicated groupsGroups 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
Evaluation of chronic toxicity and carcinogenicity of HFPO-DA in miceRegulatory toxicology and pharmacology : RTP · 2026
Summary (written by the submitters)
Transcriptomic anlayses were conducted on liver tissue from male and female CD-1 mice orally exposed to 0, 0.05, 0.1, 0.5 or 5 mg/kg-bw/day HFPO-DA (ammonium 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate; CASRN 62037-80-3) in a 18-month carcinogencity study that included a 9-month chronic toxicity phase in support of an investigation of the mode of action for HFPO-DA-mediated liver toxicity.
Read the full summary ↓
This combined chronic toxicity and carcinogenicity study complied with Good Laboratory Practice (GLP) and Organization for Economic Co-operation and Development (OECD) 453 test guidelines for combined chronic toxicity/carcinogenicity studies. Transcriptomic responses in exposed mice were compared to time-matched control mice. Pathway enrichment of differentially expressed genes, as well as benchmark dose modeling and functional classification of dose-responsive genes were conducted. A low hepatic transcriptomic response was observed in mice exposed to 0.05 or 0.1 mg/kg-bw/day HFPO-DA for 9 or 18 months. In mice exposed to 0.5 or 5 mg/kg-bw/day, the top most significantly enriched gene sets were similar in male and female mouse livers regardless of exposure duration. Upregulated gene sets were related to b-oxidation of fatty acids and fatty acid metabolism, PPAR signaling, and peroxisome signaling. Downregulated gene sets were related to innate immune responses and amino acid metabolism. Results from benchmark dose-response analysis indicate livers from male mice exposed to HFPO-DA for 9 months had the greatest transcriptomic response.
Published in
Evaluation of chronic toxicity and carcinogenicity of HFPO-DA in mice
Thompson CM, Heintz MM, Cullen JM et al. · Regulatory toxicology and pharmacology : RTP 2026 · PMID 41391658 · doi:10.1016/j.yrtph.2025.106014
This dataset
Open GSE250389 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 GSE250389_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 PRJNA1053795 and SRA study SRP478475. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41391658) ↗
Study design
92 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 92 sample titles: 92 distinct titles with little repetition. 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

+ 52 more — browse all 92 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.