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A Robust Mouse Liver Organoid Platform Enables Sustained Multicellular Maturation and Fibrosis Modeling from a Single Tissue Sample

GSE308085 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/02/27 Platform GPL34290Platform 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: 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
A robust mouse liver organoid platform enables sustained multicellular maturation and fibrosis modeling from a single tissue sampleScientific reports · 2026
Summary (written by the submitters)
Efficient isolation and culture of liver organoids are critical for studying liver fibrosis, liver regeneration and drug toxicity and screening. However, preserving mature hepatobiliary characteristics and concurrently incorporating fibrosis-producing hepatic stellate cells (HSCs) remains a significant challenge, often hindering the large-scale production of organoids capable of replicating key liver functions.
Read the full summary ↓
Here, we report a robust 3D organoid culture system that enables simultaneous isolation and long-term propagation of primary hepatocytes, cholangiocytes, and HSCs from a single source of mouse liver tissue. By supplementing the Hep-Medium with Notch signaling inhibitor and dexamethasone, we achieved sustained organoid maturity, including stable albumin production, metabolic activity, and liver-specific gene expression, over multiple passages in culture. Quiescent HSCs within the system retained lipid droplets and could be activated into a myofibroblast-like phenotype, also called activated HSCs, via TGFβ stimulation. Activated HSCs impaired the proliferation and stemness, and induced epithelial-mesenchymal transition (EMT) of Hep-Orgs and Cho-Orgs, enabling in vitro liver fibrosis modeling. Optimized for minimal tissue input, this platform maximizes tissue utilization efficiency while preserving the liver’s heterogeneous cellular architecture. Its versatility supports diverse applications in liver disease modeling, drug discovery, and regenerative medicine.
Published in
A robust mouse liver organoid platform enables sustained multicellular maturation and fibrosis modeling from a single tissue sample
Liang Y, Ye Y, Xie H et al. · Scientific reports 2026 · PMID 41857098 · doi:10.1038/s41598-026-42990-2
This dataset
Open GSE308085 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 GSE308085_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 PRJNA1328719 and SRA study SRP620493. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41857098) ↗
Study design
7 conditions, mostly in triplicate
Hep-Orgs P1 ×3 Hep-Orgs P5 ×3 Hep-Orgs P10 ×3 Primary hepatocytes ×3 Cho-org-P0-M ×3 Cho-org-P5-M ×3 Cho-org-P10-M ×3 Grape_like_hep_org ×1 +2 more

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 24 sample titles; they account for 21 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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