Fig. 5

Characterization of transcriptomic profile alterations with vascularization in vascular-related-like cell (VLC) subtypes. A UMAP for each sample of VLC. B Marker expression of vascular cells (CLDN5, endothelial cells; ACTA2, smooth muscle cells; COL1A1, fibroblast; RGS5, pericytes). C UMAP assigned to cell types based on unbiased gene expression profiles [See Additional file 11: Fig. S8A for clusters to which cell types are assigned; Additional file 11: Fig. S8C and S8D show the annotation]. D Endothelial cell marker expression. E Proportion of cells in each subtypes per sample. F Volcano plot of genes altered by vascularization in the CLDN5⁺ endothelial-like (ECL) cells. The data for organoids co-cultured with HUVECs for 100 days are not shown due to the low number of genes altered by vascularization. G Differentially expressed genes in VOr ECL cells (CLDN5⁺, KDR⁺, FLT1⁺) compared to endothelial cells in the fetal brain. The larger the averaged log₂(FC), the more enriched in VOr, and vice versa. H Gene expression specific to an ependymal-like (EPL) cluster. Genes colored in red represent highly expressed genes in EPL compared to other clusters, and genes colored in blue represent less expressed genes