Single-cell RNA seq analysis of mouse early E8.5 cranial tissues. (A) Schematic of experimental design. Wnt1-Cre;RosaeYFP and Mef2c-F10N-LacZ embryos with between 7-9 somites (6 each) were dissected and cranial tissues anterior to rhombomere 3 were collected. Tissues were dissociated into single cell suspensions before being processed through the 10X Genomics pipeline. The final dataset used for analysis consisted of 21,190 cells (12,498 cells from Wnt1-Cre;RosaeYFP and 8,692 from Mef2c-F10N-LacZ) and 29,041 genes. (B) YFP and LacZ staining of E8.5 Wnt1-Cre;RosaeYFP and Mef2c-F10N-LacZ embryos and 10um cranial transverse sections. YFP (green) labels cells located in the dorsal neuroepithelium and their lineages. As a result, both premigratory and migratory NCC are marked by YFP expression. LacZ (blue) labels migratory NCC. (C) Uniform Manifold Approximation and Projection (UMAP) and clustering of 6 major tissue types in the cranial region of E8.5 mouse embryos: cranial NCC, neuroectoderm, non-neural ectoderm, mesoderm, endothelial cells, and embryonic blood cells. (D) Dotplot showing the expression of tissue specific markers used for cluster identification. Dot size indicates the percentage of cells in each corresponding cluster (y-axis) that expresses a specific gene (x-axis). Dot color intensity indicates the average expression level of a specific gene in a cell cluster.