GEO series

Purification protocol of hypertrophied hepatic stellate cells from CDAHFD mice liver for their transcriptomic characterization

GSE294603 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2026/05/15 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 10 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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: 10 samples
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: Purification and Transcriptomic Characterization of Hypertrophied Hepatic Stellate Cells From CDAHFD Mouse LiverFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026

Summary (written by the submitters)

Hepatic stellate cells (HSC) are known for their major role in hepatic fibrosis. Recently, it has been shown that different subpopulations of HSC co-exist during fibrogenesis and play different roles in the establishment of fibrosis. We previously highlighted, in murine model and human biopsies, a specific subpopulation of hypertrophied HSC (hypHSC) which exhibit exacerbated retinoid droplets and were closely associated to collagen fibers.

Read the full summary ↓

The present study describes the purification protocol of hypHSC developed from a murine model of metabolic liver fibrosis. Liver dissociation followed by density gradient and fluorescence assisted cell sorting allowed us to obtain higlhly pure hypHSC preparations. Then, a transcriptomic analysis (bulk RNAseq) of hypHSCs versus quiescent HSCs purified from healthy mouse liver, was performed and showed that the hypHSCs molecular signature differs from HSC subtypes already described in the literature, with a “hybrid” profile of both inflammation and matrix remodeling. Our study highlights that a phenotype-to-molecular approach can provide complementary elements to single-cell molecular approaches.

Published in

Purification and Transcriptomic Characterization of Hypertrophied Hepatic Stellate Cells From CDAHFD Mouse Liver

Heckmann M, Djerir NE, Greliche K et al. · FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2026 · PMID 42024003 · doi:10.1096/fj.202502655RR

This dataset

Open GSE294603 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 GSE294603_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 PRJNA1250589 and SRA study SRP578585. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42024003) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE271914 Hepatic transcriptome analysis of WT and PRDX1Cys52Ser mutant mice on CDAHFD 6 samples shares cdahfd, hepatic
GSE314148 Hetereogenity of liver Treg in the CDAHFD model of MASH 1 samples shares cdahfd, liver
GSE51577 Comparative high density microarray analysis of global 5hmC patterns in mouse brain and liver following independent affinity based enrichment protocols. 9 samples shares protocol, liver
GSE278017 Susceptibility and Transcriptional Characteristics of C57BL/6 and ICR Mouse Strains in CDAHFD-Induced NASH Models 12 samples shares cdahfd
GSE249630 Modeling T cell temporal response to cancer immunotherapy rationalize development of combinatorial treatments protocols 1372 samples shares protocol
GSE250140 Comparative translating ribosome affinity purification-RNAseq (TRAPseq) by lung cell-specific drivers 49 samples shares purification
GSE298835 Leveraging dynamic cell responses to design new protocols for pluripotency maintenance 21 samples shares protocol
GSE273092 Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling (Zfp697 skeletal muscle knockout RNA-Seq of unloading-reloading protocol) 18 samples shares protocol

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.