Cardiac outflow tract (OFT) is a major hotspot for congenital heart diseases (CHDs). Approximately 30% of CHDs involve abnormalities in OFT development, which constitute a large class of CHDs, namely OFT malformations. A thorough understanding of the cellular diversity, transitions and regulatory networks of normal OFT development is essential to decipher the etiology of OFT malformations.

We preformed single-cell transcriptomic sequencing of 55,611 mouse OFT cells from three successive developmental stages that generally correspond to the early, middle and late stages of OFT remodeling and septation (47, 49 and 51 pairs of somites). We provide a single-cell reference map of cell states for normal OFT development, which allows the CHD community to assess how perturbations affect the transcriptomic states of OFT cell lineages, to prioritize candidate genes of OFT malformations based on expression, and to map candidate genes to cell types or subpopulations.

To facilitate further data exploration, we developed web-based interfaces, which permit interactive examination of expression for any gene of interest, dynamic changes in cell states for each cluster in a 3D space, and potential intercellular communications among cell lineages for any ligand-receptor pair.

For more information, please see our manuscript. Biorxiv