GEO series

Transcriptional profiling of bulk liver tissue from male and female PPARa knockout mice and mice expressing a human PPARa transgene following treatment with PFOA or vehicle drinking water in conjunction with an American diet

GSE290187 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2025/12/30 Platform GPL28457

At a glance

RNA-seq (gene expression) · mouse · 20 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: 20 samples: 7 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: Integrated assessment of the effects of PFOA exposure on hepatic transcriptome and lipid profiles in mice expressing human PPARαToxicology and applied pharmacology · 2026

Summary (written by the submitters)

Per- and polyfluoroalkyl substances (PFAS) are a family of persistent chemicals that have been released pervasively in the environment leading to widespread human exposure. Emerging epidemiological evidence shows adverse effects on liver lipids, however the extent of this impact and the mechanisms through which PFAS disrupt hepatic lipid homeostasis in humans are not well understood.

Read the full summary ↓

Here, we examine the effects of perfluorooctanoic acid (PFOA) on liver lipid profiles and probe transcriptional mechanisms contributing to liver lipid dysregulation in mice expressing human peroxisome proliferator activated receptor a (PPARa) in comparison to PPARa null mice. Male and female mice were fed a What We Eat In America diet and exposed to PFOA via drinking water for 6 weeks. Serum PFOA concentrations averaged 48 ± 9 μg/mL. Across male and female hPPARa mice, PFOA increased liver total lipids and total triacylglycerides, which was stronger in males than females and largely dependent on hPPARa. Additional lipid class strongly altered by PFOA exposure predominantly belong to phosphatidylcholine and sphingolipid classes. PFOA significantly decreased sphingomyelin abundance and increased ceramide abundance regardless of genotype, which coincided with an increase in expression of SMase, the enzyme that converts sphingomyelin to ceramide. PFOA changed the expression of ~2,000 hepatic genes with a larger impact in hPPARa versus PPARa null mice. In this human-relevant PFOA exposure scenario, less than 60% of transcriptional changes induced by PFOA depended on PPARa expression. CAR appears to be another major molecular initiating event, with other transcription factors pathways more likely to be modulated downstream, including PPARg, pregnane X receptor, estrogen receptor a, farnesoid X receptor, and pregnane X receptor. These results highlight the ability of PFOA to modulate liver lipids beyond triacylglycerides and the need to further refine our understanding of the molecular initiating and downstream transcriptional regulators in PFAS-induced mechanisms of action.

Published in

Integrated assessment of the effects of PFOA exposure on hepatic transcriptome and lipid profiles in mice expressing human PPARα

Nielsen G, Reed E, Lara B et al. · Toxicology and applied pharmacology 2026 · PMID 41297771 · doi:10.1016/j.taap.2025.117658

This dataset

Open GSE290187 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 GSE290187_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 PRJNA1226539 and SRA study SRP565486. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41297771) ↗

Study design

7 conditions, mostly in triplicate

F_hPPARa_Vh ×3 M_hPPARa_PFOA ×3 F_KO_PFOA ×3 M_KO_Vh ×3 M_KO_PFOA ×3 M_hPPARa_Vh ×2 F_hPPARa_PFOA ×2 F_KO_Vh ×1

Supports a between-group comparison across 19 samples.

How we read this: 7 replicated groups read from 20 sample titles; they account for 19 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

GSM8807914 F_hPPARa_Vh_R1 F_hPPARa_Vh
GSM8807915 M_hPPARa_Vh_R1 M_hPPARa_Vh
GSM8807916 M_hPPARa_PFOA_R1 M_hPPARa_PFOA
GSM8807917 M_hPPARa_Vh_R2 M_hPPARa_Vh
GSM8807918 F_hPPARa_Vh_R2 F_hPPARa_Vh
GSM8807919 F_hPPARa_Vh_R3 F_hPPARa_Vh
GSM8807920 M_hPPARa_PFOA_R2 M_hPPARa_PFOA
GSM8807921 F_hPPARa_PFOA_R1 F_hPPARa_PFOA
GSM8807922 F_hPPARa_PFOA_R2 F_hPPARa_PFOA
GSM8807923 M_hPPARa_PFOA_R3 M_hPPARa_PFOA
GSM8807924 F_KO_PFOA_R1 F_KO_PFOA
GSM8807925 M_KO_Vh_R1 M_KO_Vh
GSM8807926 M_KO_Vh_R2 M_KO_Vh
GSM8807927 M_KO_PFOA_R1 M_KO_PFOA
GSM8807928 F_KO_PFOA_R2 F_KO_PFOA
GSM8807929 F_KO_PFOA_R3 F_KO_PFOA
GSM8807930 M_KO_PFOA_R2 M_KO_PFOA
GSM8807931 M_KO_PFOA_R3 M_KO_PFOA
GSM8807932 M_KO_Vh_R3 M_KO_Vh
GSM8807933 F_KO_Vh_R1

Datasets on a similar topic

GSE239392 Transcriptomic analysis of gene diffrentially expressed after Pemafibrate treatment on the livers of mice overexpressing FAT10. 16 samples shares expressing, treatment
GSE276922 Using RNA-seq to analyze gene expression in the mouse lens epithelial cells alpha-TN4 overexpressing Vector, WT-CREB, KCREB, R314A-CREB, S133A-CREB, S133A-KCREB and S133A/R314A -CREB before and after TGFβ treatment 14 samples shares expressing, treatment
GSE264124 Single Cell RNA sequencing of the non-tumor components of the tumor mass after either empty vector control or Zbtb46 overexpressing lentiviral intratumoral treatments 2 samples shares expressing, treatment
GSE308174 Bulk mRNA-seq analysis of mouse skeletal muscle, heart and liver expressing wild-type and mutant H2B 75 samples shares expressing
GSE268241 HPV16-expressing tumors release multiple IL-1 ligands to orchestrate systemic immunosuppression whose disruption enables efficacy of a therapeutic vaccine. 63 samples shares expressing
GSE275643 Single cell RNA-seq reveals GINIP-Expressing neurons as the main targets of focused ultrasoud. 57 samples shares expressing
GSE309843 RNAseq data of frontal cortex of 4 months high fat diet fed WT, AKO, 4 months high fat diet fed conditional human amylin expressing mice followed by vehicle and Tamoxifen injection, and 2 months high fat diet fed WT mice 49 samples shares expressing
GSE266395 Acetaminophen overdose reveals protease activated receptor 4 as a low expressing but potent receptor on the hepatic endothelium in mice 48 samples shares expressing

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.