GEO series

Generation of hESC-derived expandable hepatoblast organoids and their derivatives of functional polarized hepatocyte organoids under 3D suspended culture conditions

GSE239550 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2024/12/30 Platform GPL20795

At a glance

Single-cell RNA-seq · human · 15 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: Homo sapiens (human)
Samples: 15 samples: 6 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: Large-Scale Production of Expandable Hepatoblast Organoids and Polarised Hepatocyte Organoids From hESCs Under 3D Static and Dynamic Suspension ConditionsCell proliferation · 2025

Summary (written by the submitters)

Background & Aims: The increasing requirements for hepatocytes in therapeutics and pharmacy call for an efficient system that enables large-scale production of functional hepatocytes in vitro. Hepatoblast (HB) hold the ability to regenerate liver when damaged, combined with organoid (org) technology, the culture of human pluripotent stem cell (hPSCs) derived HB-orgs was established under 2D culture system, enabling long-term expansion of HB in vitro.

Read the full summary ↓

However, the expensive cost and the limitation of existing methods impede the further scale up of the production. Methods: Under 3D suspension culture conditions with the support of Matrigel at low concentration in conjunction with employing the developed (defined) medium, we developed a novel system to efficiently and reproducibly generate expandable HB-orgs and functional polarized hepatocyte organoids (P-hep-orgs) derived from hESCs. HB-orgs were further scaled up by dynamic culture in spinner flasks, and the maturity and function of P-hep-orgs was validated by transcriptome analysis and in vitro and in vivo hepatic functional assays. scRNA-seq was used to further profile HB-orgs and P-hep-orgs. Results: Our HB-orgs exhibited biopotency that could differentiate into functional hepatocytes and cholangiocytes. They proliferated actively at least for 15 passages with defined medium through avoiding the excessive autophagy under 3D suspension culture condition. HB-orgs showed higher proliferation rate in dynamic culture conditions and could reach 10^12 cell number at the initiate number of 3 million cells in only 4 weeks. With further differentiation, P-hep-orgs displayed characteristics of hepatocytes in liver, including the polarization state which mediated by integrin-AMPK signalling pathway, molecular features and improved liver functions. Moreover, P-hep-orgs were used for predicting the toxicity of various compounds, and modeling the development of hepatic lipid accumulation, as well as rescuing acute liver failure of mice. Conclusion: Our work provided a cost-efficient method for large-scale generation of 3D HB-orgs and 3D P-hep-orgs that hold considerable potential to be a robust platform for disease research, drug screening/development and toxic study, as well as clinical applications.

Published in

Large-Scale Production of Expandable Hepatoblast Organoids and Polarised Hepatocyte Organoids From hESCs Under 3D Static and Dynamic Suspension Conditions

Wu H, Wang J, Liu S et al. · Cell proliferation 2025 · PMID 39921573 · doi:10.1111/cpr.70001

This dataset

Open GSE239550 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 GSE239550_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 PRJNA999677. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39921573) ↗

Study design

6 conditions, mostly in triplicate

MG- Hborg biol ×3 MG+ Hborg biol ×3 Pheporg biol ×3 H9 biol ×2 Nphepsphere biol ×2 PHH biol ×2

Supports a between-group comparison across 15 samples.

How we read this: 6 replicated groups read from 15 sample titles; they account for 15 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

GSM7667159 H9 biol rep 1 H9 biol
GSM7667160 H9 biol rep 2 H9 biol
GSM7667161 MG- Hborg biol rep 1 MG- Hborg biol
GSM7667162 MG- Hborg biol rep 2 MG- Hborg biol
GSM7667163 MG- Hborg biol rep 3 MG- Hborg biol
GSM7667164 MG+ Hborg biol rep 1 MG+ Hborg biol
GSM7667165 MG+ Hborg biol rep 2 MG+ Hborg biol
GSM7667166 MG+ Hborg biol rep 3 MG+ Hborg biol
GSM7667167 Nphepsphere biol rep 1 Nphepsphere biol
GSM7667168 Nphepsphere biol rep 2 Nphepsphere biol
GSM7667169 Pheporg biol rep 1 Pheporg biol
GSM7667170 Pheporg biol rep 2 Pheporg biol
GSM7667171 Pheporg biol rep 3 Pheporg biol
GSM7667172 PHH biol rep 1 PHH biol
GSM7667173 PHH biol rep 2 PHH biol

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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.