Fig. 9: scRNAseq analysis of Cep83 and Fgf10 tKO cortical populations in folded regions.
From: Cortex folding by combined progenitor expansion and adhesion-controlled neuronal migration
a Scheme of tissue collection for scRNAseq. Areas indicated by dashed line were manually dissected from coronal sections of E15.5 rostral to medial cortex. Three Cep83 tKO brains (one with sulcus), three Fgf10 tKO brains (one with gyrus), n = 2 littermate CTLs each were collected for tissue preparation. b UMAP clustering of cells from E15.5 Cep83 tKO (n = 19267), Fgf10 tKO (n = 14777), CTL (n = 22107) embryos classified as projection neurons (n = 40900), apical progenitors (n = 9212), interneurons (n = 2778), intermediate progenitors (n = 1474), endothelial cells (n = 1357), and microglia (n = 531). c Proportions of each cell type by genotype in CTL and Cep83 tKO mice. d Expression of the IP marker gene Eomes (Tbr2) in intermediate progenitor cell type for CTL and Cep83 tKO embryos. (UMAP and violin plot). e UMAP clustering of projection neurons with annotated subpopulations, upper layer neurons (n = 17963), immature neurons (n = 10103), lower layer neurons (n = 6897), and newborn neurons (n = 5937). f Proportions of subpopulations by genotype in CTL and Cep83 tKO embryos. Chi-Square test. g Expression of CP layer marker gene, Satb2, in upper layer neurons for CTL and Cep83 tKO embryos. (UMAP and violin plots). h UMAP clustering for Cep83 tKO embryo in sulcus area and for Fgf10 tKO embryo in gyrus area. i Quantification of Flrt3+ cells in apical progenitors, intermediate progenitors, and projection neurons in the sulcus area of the Cep83 tKO embryo and in the gyrus area of the Fgf10 tKO embryo. Chi-Square test.
