Understanding the development of oral epithelial organs through single cell transcriptomic analysis

During vertebrate craniofacial development, the oral epithelium begins as a simple and morphologically homogeneous tissue. It then gives rise to locally complex structures, including the developing teeth, salivary glands, and taste buds. While there is significant knowledge about the molecular mechanisms regulating the morphogenesis of these organs at later stages, how the epithelium is initially patterned and specified to generate diverse cell types and organs remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations, we conducted single cell RNA-sequencing using mandibular epithelia from embryonic day (E) 12.0 mouse embryos and whole mandibles from E9.5 mouse embryos. The goal of this study is therefore to generate a detailed transcriptional atlas of the developing mandibular epithelium. Overall design: For the E12.0 epithelial dataset, mandibular epithelial cells from six K14Cre;R26mT/mG mouse embryos from the same litter were separated from the mesenchyme, dissociated and sorted using fluorescence-activated cell sorting (FACS) to isolate GFP+ single epithelial cells. The single pooled population was analyzed using 10X scRNA-seq. For the E9.5 dataset, mandibular arches including both the epithelium and mesenchyme were dissected from eight embryos and dissociated. The single pooled population was analyzed using 10X scRNA-seq.