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Concerted Actions of FoxO1 and Pparα in hepatic gene expression and metabolic adaptation

GSE282595 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/11/13 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 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
Concerted Actions of FoxO1 and PPARα in Hepatic Gene Expression and Metabolic AdaptationDiabetes · 2025
Summary (written by the submitters)
Several transcription factors regulate the fasting response in the liver. They include FoxO1 and 3, cAMP response element binding protein (CREB), CCAAT enhancer-binding proteins (CEBP α/ β), glucocorticoid receptor (GR), Pparα, FoxA2, HNF4α, and many others. Previous genome-wide chromatin occupancy studies demonstrated an unexpected overlap of FoxO1 and PPARα DNA binding sites at active intergenic and intron enhancers, where approximately half of FoxO1 sites are shared with PPARα.
Read the full summary ↓
However, the functional significance of these findings remains unknown. To address this gap in knowledge, we performed molecular interaction analyses of these two transcription factors and generated a combined hepatocyte-specific ablation of the respective genes. We found a concerted regulation of genes involved in glucose metabolism, with additive effects on in vivo tests of glucose tolerance. The data reveal a heretofore unexplored functional relay of two critical transcriptional networks in liver metabolism.
Published in
Concerted Actions of FoxO1 and PPARα in Hepatic Gene Expression and Metabolic Adaptation
Kitamoto T, Watanabe H, Miyachi Y et al. · Diabetes 2025 · PMID 40680014 · doi:10.2337/db24-1173
This dataset
Open GSE282595 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 GSE282595_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 PRJNA1189443 and SRA study SRP546986. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40680014) ↗
Study design
8 conditions, mostly in triplicate
RD_WT_Fast ×3 RD_LFKO_Fast ×3 RD_LPKO_Fast ×3 RD_LFPKO_Fast ×3 HFD_WT_Fast ×3 HFD_LFKO_Fast ×3 HFD_LPKO_Fast ×3 HFD_LFPKO_Fast ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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