High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development

The differentiation of post-migratory cranial neural crest cells (CNCCs) into distinct mesenchymal lineages is crucial for craniofacial development. Here we report a high-resolution spatiotemporal transcriptomic and cell-type atlas of CNCC-derived mesenchymal lineage diversification associated with mouse palatogenesis. We systematically defined each mesenchymal cell type by mapping their transcriptomic profiles to spatial identities. Overall design: To systematically evaluate the dynamic cell fates of all the cell populations associated with palate development, we performed scRNA-seq analysis of the tissues in the palatal region across all key stages of palatogenesis (E12.5, E13.5, E14.5, E15.5, and E18.5).