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A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages, and which maps cell type-specific gene expression to specific anatomical domains. Spatial Transcriptomics identified unique gene profiles corresponding to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA-sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001005468 Illumina HiSeq 2500 NextSeq 500 21
Publications Citations
Direct coculture of human pluripotent stem cell-derived cardiac progenitor cells with epicardial cells induces cardiomyocyte proliferation and reduces sarcomere organization.
J Mol Cell Cardiol 162: 2022 144-157
Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations.
Vasc Health Risk Manag 17: 2021 641-657
A comprehensive comparison on cell-type composition inference for spatial transcriptomics data.
Brief Bioinform 23: 2022 bbac245
A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification.
Cardiovasc Res 119: 2023 1361-1376