GEO series
Single-cell multiomic integration identifies widespread, cell-type resolved fetal reactivation in the diseased human heart
GSE290367
Homo sapiens (human)
Single-cell RNA-seq
90 samples
Submitted 2026/03/15
Platform GPL21697
At a glance
Single-cell RNA-seq · human · 90 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 90 samples: 35 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
- An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and diseaseGenome biology · 2026
Summary (written by the submitters)
Background: As the first organ to develop in utero, the human heart undergoes extensive molecular, structural and metabolic remodeling during development and must sustain its function throughout life. Results: We generate an integrated multiomic atlas of human cardiac cells, combining newly generated and publicly available single-nucleus RNA sequencing datasets from 299 donors and single nucleus ATAC-seq datasets from 106 donors.
Read the full summary ↓
Developmental and disease-associated processes drive far more extensive molecular remodeling than sex-associated or aging-dependent effects. Across nearly all cardiac cell types, developmental and disease-driven changes exhibit strong overlap at both the transcriptomic and epigenomic levels, revealing widespread reactivation of fetal-associated gene programs beyond cardiomyocytes. Both cardiac development and disease show convergent shifts in intercellular communication, including increased TGFβ signaling. Integration of gene expression and chromatin accessibility data reveals putative cell-type–specific transcriptional factors driving fetal reactivation in major cardiac diseases. Spatial transcriptomics data orthogonally identifies localization of this fetal reactivation signature within spatially distinct niches in ischemic and fibrotic zones of acute myocardial infarction. Finally, we construct a cell-type–resolved enhancer-to-gene linkage map that refines the association of dilated and hypertrophic cardiomyopathy genetic risk loci to downstream target genes. Conclusions: This study presents a comprehensive multimodal, cell-type–resolved atlas of the human heart, providing a foundation for understanding human cardiac gene regulation across the human lifespan and in cardiac diseases.
Published in
Gao W, Hu P, Wick B et al.
· Genome biology 2026
· PMID 41937210
· doi:10.1186/s13059-026-04061-7
This dataset
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.
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 GSE290367_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1227589 and SRA study SRP566068. Searching any of these in the dataset finder brings you back here.
Study design
35 conditions, mostly in duplicate
Penn_F1 donor, female, gestational week 18, n… ×5
K1783 donor, male, age 69, non-diseased, left… ×4
Penn_F2 donor, male, gestational week 18, non… ×3
K1430 donor, male, age 62, DCM, left ventricl… ×3
K1584 donor, male, age 22, non-diseased, left… ×3
ND15755 donor, male, age 65, non-diseased, ri… ×3
ND15840 donor, female, age 91, non-diseased, … ×3
ND15840 donor, female, age 91, non-diseased, … ×3
+35 more
Supports a between-group comparison across 82 samples.
How we read this: 35 replicated groups read from 90 sample titles; they account for 82 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
- GSM8811384 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 1 Penn_F1 donor, female, …
- GSM8811385 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 2 Penn_F1 donor, female, …
- GSM8811386 Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 1 Penn_F2 donor, male, ge…
- GSM8811387 Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 2 Penn_F2 donor, male, ge…
- GSM8811388 Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 1 Penn_F2 donor, male, ge…
- GSM8811389 Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 2 Penn_F2 donor, male, ge…
- GSM8811390 Penn_F1 donor, female, gestational week 18, non-diseased, atria
- GSM8811391 Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 1 Penn_F2 donor, male, ge…
- GSM8811392 Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, non-diseased, replicate 2
- GSM8811393 Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 3 Penn_F2 donor, male, ge…
- GSM8811394 Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 4 Penn_F2 donor, male, ge…
- GSM8811395 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 3 Penn_F1 donor, female, …
- GSM8811396 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 4 Penn_F1 donor, female, …
- GSM8811397 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 5 Penn_F1 donor, female, …
- GSM8811398 K1430 donor, male, age 62, DCM, left ventricle, replicate 1 K1430 donor, male, age …
- GSM8811399 K1430 donor, male, age 62, DCM, left ventricle, replicate 2
- GSM8811400 K1430 donor, male, age 62, DCM, left ventricle, replicate 3 K1430 donor, male, age …
- GSM8811401 K1430 donor, male, age 62, DCM, left ventricle, replicate 4 K1430 donor, male, age …
- GSM8811402 K1485 donor, male, age 78, non-diseased, left ventricle, replicate 1 K1485 donor, male, age …
- GSM8811403 K1485 donor, male, age 78, non-diseased, left ventricle, replicate 2 K1485 donor, male, age …
- GSM8811404 K1488 donor, male, age 81, non-diseased, left ventricle, replicate 1 K1488 donor, male, age …
- GSM8811405 K1488 donor, male, age 81, non-diseased, left ventricle, replicate 2 K1488 donor, male, age …
- GSM8811406 K1545 donor, male, age 44, non-diseased, left ventricle, replicate 1 K1545 donor, male, age …
- GSM8811407 K1545 donor, male, age 44, non-diseased, left ventricle, replicate 2 K1545 donor, male, age …
- GSM8811408 K1549 donor, male, age 49, non-diseased, left ventricle, replicate 1 K1549 donor, male, age …
- GSM8811409 K1549 donor, male, age 49, non-diseased, left ventricle, replicate 2 K1549 donor, male, age …
- GSM8811410 K1561 donor, male, age 73, non-diseased, left ventricle
- GSM8811411 K1570 donor, male, age 73, non-diseased, left ventricle, replicate 1 K1570 donor, male, age …
- GSM8811412 K1570 donor, male, age 73, non-diseased, left ventricle, replicate 2 K1570 donor, male, age …
- GSM8811413 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 1 K1584 donor, male, age …
- GSM8811414 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 2 K1584 donor, male, age …
- GSM8811415 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 3 K1584 donor, male, age …
- GSM8811416 K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 1 K1617 donor, male, age …
- GSM8811417 K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 2 K1617 donor, male, age …
- GSM8811418 K1617 donor, male, age 64, DCM, left ventricle, replicate 3 K1617 donor, male, age …
- GSM8811419 K1617 donor, male, age 64, DCM, left ventricle, replicate 4 K1617 donor, male, age …
- GSM8811420 K1622 donor, male, age 56, non-diseased, left ventricle, replicate 1 K1622 donor, male, age …
- GSM8811421 K1622 donor, male, age 56, non-diseased, left ventricle, replicate 2 K1622 donor, male, age …
- GSM8811422 K1647 donor, male, age 34, non-diseased, left ventricle, replicate 1 K1647 donor, male, age …
- GSM8811423 K1647 donor, male, age 34, non-diseased, left ventricle, replicate 2 K1647 donor, male, age …
+ 50 more — browse all 90 samples with per-sample file links →
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