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Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and PPARα knockout mouse livers

GSE282998 Mus musculus (mouse) RNA-seq (gene expression) 192 samples Submitted 2025/04/21 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 192 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
192 samples: 144 × 1528 vs 48 × CGroups 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
Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse liversToxicological sciences : an official journal of the Society of Toxicology · 2025
Summary (written by the submitters)
Recent transcriptomic analyses in vitro comparing the transcriptomic profile of the short-chain per- and polyfluoroalkyl substances (PFAS) HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate) to that of other chemicals with known MOAs add to the current weight of evidence supporting the peroxisome proliferator-activated receptor alpha (PPARa) activator-induced rodent hepatocarcinogenesis mode of action (MOA) for HFPO-DA-mediated liver effects in rodents.
Read the full summary ↓
To further inform the MOA of HFPO-DA and evaluate the PPARa-dependence of HFPO-DA-mediated liver effects in vivo, phenotypic and transcriptomic responses in wild-type (WT) and PPARa knockout (KO) mice were investigated following short-term exposure to HFPO-DA or well-established agonists of PPAR (GW7647) and PPARg (rosiglitazone), or cytotoxic agent (acetaminophen [APAP]). Phenotypic and transcriptomic assessment of mouse livers demonstrated a general lack of response to HFPO-DA or GW7647 exposure in PPARa KO but not WT mice, whereas exposure to rosiglitazone or APAP elicited similar, if not greater phenotypic and transcriptomic responses in PPARa KO mice compared to WT mice. Dose-dependent increases in liver weight and increased karyomegaly and mitosis scores via histopathology, as well as increased transcriptomic signaling related to PPARa activation and cell proliferation were observed in HFPO-DA or GW7647-exposed WT mice. The consistent phenotypic and transcriptomic signaling patterns between HFPO-DA and GW7647 in WT mice, and the lack of changes in PPARα KO mice, provide further support that HFPO-DA-mediated liver effects in mice are PPARa-dependent and occur via the PPARa MOA. Thus, these adverse effects in mice are not appropriate for use as the basis of toxicity values for human health risk assessment.
Published in
Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse livers
Heintz MM, Buerger AN, Haws LC et al. · Toxicological sciences : an official journal of the Society of Toxicology 2025 · PMID 40216583 · doi:10.1093/toxsci/kfaf049
This dataset
Open GSE282998 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 GSE282998_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 PRJNA1191425 and SRA study SRP547980. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40216583) ↗
Study design
144 × 1528 vs 48 × C

Supports a between-group comparison across 192 samples.

How we read this: 2 replicated groups read from 192 sample titles; they account for 192 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

+ 152 more — browse all 192 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.