Extended Data Fig. 5: Trajectory analysis based on scRNA-seq data.

a, Monocle-generated annotated uniform manifold approximation projection (UMAP) plots of hiSGs on Day 80. b, Feature plots for the expression of mesenchymal, epithelial, and salivary gland cell type markers in hiSGs. c, Pseudotime trajectory projected onto a UMAP in all clusters. d, Feature plots for the gene expression of ductal, acinar, and cycling cell markeres based UMAP plots of ductal-acinar lineage. e, Pseudotime trajectory projected onto a UMAP in the ductal-acinar lineage. The colour of a cell shows its cluster identity (left) and pseudotime values (right). f, Pseudotime-ordered expression of selected marker genes: AQP5, KRT8, KRT19 (ductal acinar), and MKI67 (cycling). Lines denote the relative expression of each marker in pseudotime. g, Feature plots for the gene expression of basal, myoepithelial, and cycling cell markeres based UMAP plots of basal-myoepithelial lineage. h, Pseudotime trajectory projected onto a UMAP in the basal-myoepithelial lineage. The colour of a cell shows its cluster identity (left) and pseudotime values (right). i, Pseudotime-ordered expression of selected marker genes: ACTA2, KRT14, KRT5 (basal-myoepithelial), and MKI67 (cycling). Lines denote the relative expression of each marker in pseudotime. a-h,Ten organoids were pooled for one scRNA-seq experiment.