Fig. 5

Clustering and pseudotemporal trajectories of FAPs nuclei in aged human and high IMF content pig muscles. (a) UMAP plot showing three subclusters of the isolated single nuclei from HLW and LLW muscle. (b) UMAP and violin plot displaying the expression of selected marker genes for each subcluster of nuclei. (c) Nuclear proportion in each subcluster in different species. Each cluster is color-coded. (d) Left, heatmap showing the top 10 most DEGs by bimod difference analysis algorithm (P-Value < 0.01, Log2FC ≥ 0.26) between cell types identified. Right, KEGG enrichment for marker genes of each cell type in different species. Each lane represents a subcluster. (e) Pseudotime ordering of all of the FAP/fibroblast nuclei of subcluster PDGFRA⁺ FAPs, fibroblasts, and PDE4D⁺/PDE7B⁺. The horizontal and vertical coordinates are two principal components respectively in two dimensions. Each dot represents one nucleus (color-coded by its identity), and each branch represents one cell state. Pseudotime is shown colored in a gradient from dark to light blue, and the start of pseudotime is indicated. Activation of the PDGFRA⁺ FAPs cluster can lead to PDE4D⁺/PDE7B⁺ fate. (f) Unsupervised pseudotime trajectory of the three subtypes of FAPs by RNA velocity analysis. Trajectory is colored by cell subtypes. The arrow indicates the direction of cell pseudo-temporal differentiation. (g) Distribution of marker genes of the three subtypes on the UMAPs based on RNA velocity analysis calculated differences by t-test.