GEO series
Single-cell multiomic integration identifies widespread, cell-type resolved fetal reactivation in the diseased human heart
GSE290367
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
90 samples
Submitted 2026/03/15
Platform GPL21697
Summary
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. 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
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Direct links to NCBI, no account and no request form: the whole study as GSE290367_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 90 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1227589 and SRA study SRP566068. Searching any of these in the dataset finder brings you back here.
Study design
15 conditions, mostly in duplicate
Penn_F1 donor, female, gestational week 18, n… ×5
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
Penn_F2 donor, male, gestational week 18, non… ×2
Penn_F2 donor, male, gestational week 18, non… ×2
K1485 donor, male, age 78, non-diseased, left… ×2
K1488 donor, male, age 81, non-diseased, left… ×2
+11 more
Supports a between-group comparison across 36 samples.
15 replicated groups read from the first 40 of 90 sample titles; they account for 36 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8811384 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 1
- GSM8811385 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 2
- GSM8811386 Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 1
- GSM8811387 Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 2
- GSM8811388 Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 1
- GSM8811389 Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 2
- 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
- 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
- GSM8811394 Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 4
- GSM8811395 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 3
- GSM8811396 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 4
- GSM8811397 Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 5
- GSM8811398 K1430 donor, male, age 62, DCM, left ventricle, replicate 1
- GSM8811399 K1430 donor, male, age 62, DCM, left ventricle, replicate 2
- GSM8811400 K1430 donor, male, age 62, DCM, left ventricle, replicate 3
- GSM8811401 K1430 donor, male, age 62, DCM, left ventricle, replicate 4
- GSM8811402 K1485 donor, male, age 78, non-diseased, left ventricle, replicate 1
- GSM8811403 K1485 donor, male, age 78, non-diseased, left ventricle, replicate 2
- GSM8811404 K1488 donor, male, age 81, non-diseased, left ventricle, replicate 1
- GSM8811405 K1488 donor, male, age 81, non-diseased, left ventricle, replicate 2
- GSM8811406 K1545 donor, male, age 44, non-diseased, left ventricle, replicate 1
- GSM8811407 K1545 donor, male, age 44, non-diseased, left ventricle, replicate 2
- GSM8811408 K1549 donor, male, age 49, non-diseased, left ventricle, replicate 1
- GSM8811409 K1549 donor, male, age 49, non-diseased, left ventricle, replicate 2
- GSM8811410 K1561 donor, male, age 73, non-diseased, left ventricle
- GSM8811411 K1570 donor, male, age 73, non-diseased, left ventricle, replicate 1
- GSM8811412 K1570 donor, male, age 73, non-diseased, left ventricle, replicate 2
- GSM8811413 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 1
- GSM8811414 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 2
- GSM8811415 K1584 donor, male, age 22, non-diseased, left ventricle, replicate 3
- GSM8811416 K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 1
- GSM8811417 K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 2
- GSM8811418 K1617 donor, male, age 64, DCM, left ventricle, replicate 3
- GSM8811419 K1617 donor, male, age 64, DCM, left ventricle, replicate 4
- GSM8811420 K1622 donor, male, age 56, non-diseased, left ventricle, replicate 1
- GSM8811421 K1622 donor, male, age 56, non-diseased, left ventricle, replicate 2
- GSM8811422 K1647 donor, male, age 34, non-diseased, left ventricle, replicate 1
- GSM8811423 K1647 donor, male, age 34, non-diseased, left ventricle, replicate 2
+ 50 more — browse all 90 samples with per-sample file links →
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