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. 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).