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Hypoimmunogenic hPSC-derived cardiac organoids for immune evasion and heart repair [bulkRNA-seq]

GSE299171 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/06/08 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 12 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Human pluripotent stem cell (hPSC)-derived cardiac therapies hold great promise for heart 41 regeneration but face major translational barriers due to allogeneic immune rejection. Here, we 42 engineered hypoimmunogenic hPSCs using a two-step CRISPR-Cas9 strategy: (1) B2M 43 knockout, eliminating HLA class I surface expression, and (2) knock-in of HLA-E or HLA-G trimer 44 constructs in the AAVS1 safe harbor locus to confer robust immune evasion.
Read the full summary ↓
Hypoimmunogenic 45 hPSCs maintained pluripotency, efficiently differentiated into cardiac cell types that resisted both 46 T and NK cell-mediated cytotoxicity in vitro, and self-assembled into engineered cardiac 47 organoids. Comprehensive analyses of the hypoimmunogenic cells and organoids revealed 48 preservation of transcriptomic, structural, and functional properties with minimal off-target effects 49 from gene editing. In vivo, hypoimmunogenic cardiac organoids restored contractile function in 50 infarcted rat hearts and demonstrated superior graft retention and immune evasion in humanized 51 mice compared to wild-type counterparts. These findings establish the therapeutic potential of 52 hypoimmunogenic hPSC-CMs in the cardiac organoid platform, laying the foundation for off-the shelf cardiac cell therapies to treat cardiovascular disease, the leading cause of death worldwide.
This dataset
Open GSE299171 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 GSE299171_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 PRJNA1273019 and SRA study SRP590362. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly with about 4 replicates each
UDET iCM ×4 UDET iEC ×4 UDET iECF ×4 UDET iPC ×4 UDET iPSC ×4 UDET organoid ×4 WT iCM ×4 WT iEC ×4 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.