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Human-induced pluripotent Stem Cell-Derived Hepatic Stellate Cells in Liver Organoids: Maturation Promotion and Essential Role in Vascularization

GSE249826 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2026/03/20 Platform GPL17303
At a glance

RNA-seq (gene expression) · human · 26 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
Homo sapiens (human)
Samples
26 samples: 9 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
Human pluripotent stem cell-derived fetal hepatic stellate cells promote vascularization and maturation in liver organoidsDevelopmental cell · 2026
Summary (written by the submitters)
Human-induced pluripotent stem cell (hiPSC)-derived liver organoids (LOs) are valuable for studying human liver organogenesis but face challenges in faithfully recapitulating certain processes, like vasculogenesis, due to the lack of specific cell components. Hepatic stellate cells (HSCs), which are liver-specific pericytes and might be crucial for liver vasculogenesis, remain underutilized in developmental studies because of their disease-related "activated" status and inefficient generation process.
Read the full summary ↓
Here, we present an efficient method for generating hiPSC-derived HSCs (hiPSC-HSCs) resembling non-activated HSCs in the healthy human liver. These hiPSC-HSCs exhibit exceptional expandability (>105-fold) while maintaining essential cellular features. Additionally, in entirely hiPSC-derived LOs consisting of HSCs, hepatic endoderm, and endothelial cells, hiPSC-HSCs play a vital role in LO maturation and vascularization, both in vitro and in vivo. This work represents a significant advancement in understanding HSC roles in human liver development, and LOs containing non-activated hiPSC-HSCs hold potential in modeling congenital human liver diseases.
Published in
Human pluripotent stem cell-derived fetal hepatic stellate cells promote vascularization and maturation in liver organoids
Yang X, Nie YZ, Lu C et al. · Developmental cell 2026 · PMID 41027426 · doi:10.1016/j.devcel.2025.09.002
This dataset
Open GSE249826 in finder → Find more human 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 GSE249826_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 PRJNA1050798 and SRA study SRP477185. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41027426) ↗
Study design
9 conditions, mostly in triplicate
hiPSC-STM ×3 hiPSC-HSC P0 ×3 pHSC ×3 hiPSC-HSC P1 ×3 hiPSC-HSC P3 ×3 hiPSC-HSC P6 ×3 hiPSC-HE ×3 hiPSC-EC ×3 +1 more

Supports a between-group comparison across 26 samples.

How we read this: 9 replicated groups read from 26 sample titles; they account for 26 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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