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Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish]

GSE241156 Danio rerio (zebrafish) RNA-seq (gene expression) 14 samples Submitted 2024/11/15 Platform GPL20828Platform GPL19057
At a glance

RNA-seq (gene expression) · zebrafish · 14 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
Danio rerio (zebrafish)
Samples
14 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
Cross-species comparison reveals that Hmga1 reduces H3K27me3 levels to promote cardiomyocyte proliferation and cardiac regenerationNature cardiovascular research · 2025
Summary (written by the submitters)
The prospect of repairing the heart after a myocardial infarction by promoting cardiomyocyte proliferation has gained momentum from studies showing the heart's regenerative ability in fish, amphibians and neonatal mammals. Despite evidence of varying cardiomyocyte proliferation rates among species, the molecular mechanisms driving cardiomyocyte cell cycle re-entry remain insufficiently understood.
Read the full summary ↓
In this study, we employed spatial transcriptomics and identified high-mobility group AT-hook 1a (Hmga1a) as being upregulated in cardiomyocytes of the injury border zone in zebrafish, but not in mice. Through knock-out and cardiomyocyte-specific overexpression of hmga1a, we found that Hmga1a was required for zebrafish heart regeneration and sufficient to drive cardiomyocyte proliferation. In addition, a single injection of Hmga1 virus in injured mouse hearts resulted in increased border zone cardiomyocyte proliferation and improved heart function. Mechanistically, Hmga1 expression reduced repressive H3K27me3 histone modifications from developmentally-regulated genes and induced a border zone-like transcriptional program in adult cardiomyocytes. Our study demonstrates the value of interspecies comparisons by identifying Hmga1 as a critical driver of heart regeneration and highlights Hmga1 as a promising therapeutic candidate to improve cardiac repair after injury.
Published in
Cross-species comparison reveals that Hmga1 reduces H3K27me3 levels to promote cardiomyocyte proliferation and cardiac regeneration
Bouwman M, de Bakker DEM, Honkoop H et al. · Nature cardiovascular research 2025 · PMID 39747457 · doi:10.1038/s44161-024-00588-9
This dataset
Open GSE241156 in finder → Find more 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 GSE241156_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 PRJNA1006660 and SRA study SRP455780. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39747457) ↗
Study design
5 conditions, mostly in triplicate
zebrafish 3dpi heart ×3 zebrafish 7dpi heart ×3 zebrafish 14dpi heart ×3 mouse 7dpi_heart ×2 mouse 14dpi_heart ×2 mouse 3dpi_heart ×1

Supports a between-group comparison across 13 samples.

How we read this: 5 replicated groups read from 14 sample titles; they account for 13 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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