Fig. 3
Reconstruction of multilineage differentiation trajectories in ligament cells. a UMAP visualization of ligament cells, endothelial cells, and pericyte subclusters. The cells were clustered into 9 distinct clusters, denoted based on their differentiation stage and cell type. b Dot plots illustrating marker genes specific to various cell clusters. The color bar represents the expression level of each gene, with darker colors indicating higher expression. The size of the dots corresponds to the percentage of cells expressing the respective gene. c UMAP embedding of RNA velocity of ligament cells indicates the transition from C6_progenitor to endothelial, cartilage, and osteoblast cells. d Plot displaying the cytoTRACE pseudotime order for each cluster, where the cytoTRACE score represents the differentiation stage. e Heatmap presenting the scaled mean expression of modules consisting of co-regulated genes, organized by Louvain community analysis across the subclusters. The color bar represents the expression level of each gene, with darker colors representing higher expression. f Pseudotime kinetics of the indicated genes in the modules from (e), showcasing their expression patterns along the trajectories towards endothelial differentiation. g Histogram demonstrating the enriched pathways, identified by ReactomePA, associated with each module indicated in (e)
