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Billion-Scale production of functional hiPSC-derived cardiomyocytes in bioreactors through oxygen control and Wnt Activation

GSE272037 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/03/03 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 5 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
Billion-Scale Expansion of Functional hiPSC-Derived Cardiomyocytes in Bioreactors Through Oxygen Control and Continuous Wnt ActivationAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
Summary (written by the submitters)
Producing therapeutic quantities of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) for myocardial infarction treatment remains a significant challenge. We demonstrate that precise control of dissolved oxygen (DO) at low levels combined with Wnt pathway activation, through continuous perfusion of CHIR99021, enables the production of billions of functional hiPSC-CM in stirred-tank bioreactors (STB).
Read the full summary ↓
Specifically, culturing hiPSC-CM aggregates under 10%O2 led to an upregulation of pathways involved in cell proliferation and survival, resulting in a significantly higher hiPSC-CM expansion factor when compared to hiPSC-CM under atmospheric normoxia and static culture systems. Scaling up the process to a 2L STB, while maintaining constant power input per volume, generated 4 billion highly pure hiPSC-CM, with more than 90% positive-cells for cardiac markers. hiPSC-CM aggregates also showed spontaneous beating, expression of cardiac markers and were able to further mature in culture, revealing improved gene expression, sarcomere alignment and cardiac action potential.
Published in
Billion-Scale Expansion of Functional hiPSC-Derived Cardiomyocytes in Bioreactors Through Oxygen Control and Continuous Wnt Activation
Vicente P, Inocêncio LR, Ullate-Agote A et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 · PMID 39846380 · doi:10.1002/advs.202410510
This dataset
Open GSE272037 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 GSE272037_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 PRJNA1134750 and SRA study SRP519370. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39846380) ↗
Study design
5 conditions, mostly in triplicate
hiPSC-CMs 11 days after differentiation ×3 hiPSC-CMs expanded in T-flasks for 11 days ×3 hiPSC-CMs expanded in bioreactor in mild hypo… ×3 hiPSC-CMs expanded in bioreactor in normoxia … ×3 hiPSC-CMs cultured for two weeks after expans… ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 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
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