Fig. 5

Spatial transcriptomics with scRNA-seq present new cell types and molecular markers in human embryonic development. a scRNA-seq analysis of cardiac embryonic tissue shows three types cardiomyocytes (cardiac neural crest cells & Schwann progenitor cells, epicardial cells, ventricular and atrial cardiomyocytes), two types of endothelial cells (capillary endothelium, endothelium/pericytes/adventia) and four types of fibroblast-like cells (related to cardiac skeleton connective tissue, smaller vascular development, smooth muscle cells, larger vascular development). Spatial transcriptome combined with scRNA-seq reveals location distribution and gene markers of each cell type. Cell types and genes are screened based on the reference,¹⁰⁴ combined with differentially expressed genes in scRNA-Seq clusters and spatially heterogeneous gene panel. b GO (BP: biological process) analysis of heart cell type-specific genes and protein interaction networks (https://cn.string-db.org/). c Spatiotemporal analysis of human intestinal development at single-cell resolution identify nine intestinal compartments including epithelial, fibroblast, endothelial, pericytes, neural, muscularis, mesothelium, myofibroblast, and immune cells. Each type cells have specific gene markers, of which some have location and time-point differences in gene expression. FABP1 expresses specifically in epithelial cells and over-expresses in colon. HMGA2, MYH11, and PHOX2B down-express consistently in colon and terminal ileum. Intestinal cell signature genes are identified according to Supplemental Table 1 of the reference,¹⁰⁵ which exhibit specific key genes expression in each cell types. d GO (BP: biological process) analysis of intestinal cell type-specific genes and protein interaction networks (https://cn.string-db.org/)