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Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [bulk_isolated_cells]

GSE256502 Mus musculus (mouse) Single-nucleus RNA-seq 31 samples Submitted 2024/09/24 Platform GPL17021
At a glance

Single-nucleus RNA-seq · mouse · 31 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
31 samples: 8 conditions, mostly with about 4 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
Sex differences in murine MASH induced by a fructose-palmitate-cholesterol-enriched dietJHEP reports : innovation in hepatology · 2025
Summary (written by the submitters)
To study sex differences in the response to NASH in mice, single nucleus RNA sequencing of livers was performed. Single nucleus RNAseq demonstrated enrichment of differentially-expressed genes particularly in hepatocytes and stellate cells in females versus males fed FPC-NASH. Multiple regulons (transcription factors and target genes) implicated in lipid and other metabolic processes and hormone signaling (hepatocytes) and cell-cell communication and cell adhesion (stellate cells) were noted, which were enriched in female versus male FPC-NASH diet.
Read the full summary ↓
Bulk liver RNAseq and RNAseq of isolated hepatocytes and hepatic stellate cells were analyzed as validation experiments.
Published in
Sex differences in murine MASH induced by a fructose-palmitate-cholesterol-enriched diet
Arivazhagan L, Delbare S, Wilson RA et al. · JHEP reports : innovation in hepatology 2025 · PMID 39911943 · doi:10.1016/j.jhepr.2024.101222
This dataset
Open GSE256502 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 GSE256502_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1079799 and SRA study SRP491431. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39911943) ↗
Study design
8 conditions, mostly with about 4 replicates each
Hepato_Female_Chow ×4 Hepato_Female_NASH ×4 Hepato_Male_Chow ×4 Hepato_Male_NASH ×4 HSC_Female_NASH ×4 HSC_Male_Chow ×4 HSC_Male_NASH ×4 HSC_Female_Chow ×3

Supports a between-group comparison across 31 samples.

How we read this: 8 replicated groups read from 31 sample titles; they account for 31 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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