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co-cultures of mesenchymal cells with epithelial organoids promote fusion into bioengineered liver tissues by ECM remodeling

GSE301846 Homo sapiens (human) RNA-seq (gene expression) 31 samples Submitted 2026/08/05 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 31 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
31 samples: 12 conditions, mostly in duplicateGroups 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
Integrated mesenchymal and extracellular cues drive bioengineered liver tissue formation and functionMaterials today. Bio · 2026
Summary (written by the submitters)
Human liver tissue engineering holds promise for transplantation but faces challenges replicating liver complexity. In the present study, we created bioengineered liver tissues (BLTs) utilizing three different cell types; human intrahepatic cholangiocyte organoids (ICOs), hepatic stellate cells (HSCs), and mesenchymal stromal cells (MSCs).
Read the full summary ↓
Co-culturing with HSCs and MSCs accelerated growthand spontaneous fusion resulted in complex liver-like tissue structures. In a dynamic suspension culture, BLTs had a more compact morphology and higher expression of hepatic markers, including ALB, CYP3A4, and MRP2. We further showed that animal-derived Matrigel can be replaced by a synthetic polyisocyanide (PIC)-based hydrogel for BLTs. Importantly, PIC-based hydrogel further promoted the maturation of BLTs assessed by parameters as intracellular protein levels, morphological analysis, and metabolic activity. Transcriptomic analyses revealed mechanisms underlying tissue formation and function. To conclude, our strategy yields functional liver tissues suitable for disease modelling, drug screening, and toxicity tests, and form an important basis for future development of larger liver tissues for in vivo transplantation.
Published in
Integrated mesenchymal and extracellular cues drive bioengineered liver tissue formation and function
Ye S, Wang Z, Dirk Delemarre M et al. · Materials today. Bio 2026 · PMID 42326070 · doi:10.1016/j.mtbio.2026.103328
This dataset
Open GSE301846 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 GSE301846_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 PRJNA1287643 and SRA study SRP598868. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42326070) ↗
Study design
12 conditions, mostly in duplicate
donor1;PCOSM;D ×2 donor3;MGOSM;D ×2 donor2;MGOSM;D ×2 donor1;MGO;D ×2 donor4;PCOSM;D ×2 donor3;MGO;D ×2 donor2;MGO;D ×2 donor2;PCOSM;D ×2 +11 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 31 sample titles; they account for 24 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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