Extended Data Fig. 12: Gene dynamics in the myogenic trajectory.

a, Genes that are differentially expressed between the Myf5 path and the Myod path highlighted in Fig. 6. Cells along each path were compared using Monocle’s differentialGeneTest function. Pseudotimes along each path were scaled from 0 to 100 independently. The full model formula was ‘~path ∗ sm.ns(Pseudotime, df=3)’, whereas the reduced model was ‘~sm.ns(Pseudotime, df=3)’. Differentially expressed genes (FDR <1%, one-sided likelihood ratio test with multiple comparisons adjusted) were clustered via Ward’s method and visualized as a heat map via the pheatmap package. b, Pseudotemporal kinetics for selected genes involved in Robo–Slit signalling. Red indicates cells on the Myod1 path, while blue corresponds to the Myf5 path. Standardized expression scores for each gene on the original myogenic trajectory are shown next to the expression curves for each. Only cells with detectable expression are rendered, to prevent overplotting. c, Modules of genes differentially expressed over the myogenic trajectory. A total of 2,908 genes were clustered via hierarchical clustering. The dendrogram was cut into 14 modules using the cutree function in R, and the aggregate expression of genes in each module was computed. Colours indicate aggregate UMI counts for each module that have been scaled for library size, log-transformed and then mapped to Z-scores to enable comparison between modules. Cells with no expression of a given module are excluded to prevent overplotting.