Extended Data Fig. 5: Differentially expressed genes between myocyte clusters.

a, Volcano plot of differentially expressed genes (DEGs) between early and late pseudotime clusters in the control trajectory (Myocyte_4 vs. Myocyte_1, left) and the KO trajectory (Myocyte_5 vs. Myocyte_6; right). Wilcoxon rank sum test, Bonferroni correction. b. MA plot of RNA-seq experiment comparing P0 and P28 aCMs. c-d. Volcano plots shown in (a) overlayed with genes enriched in P28 and P0 aCMs. Wilcoxon rank sum test, Bonferroni correction. e. The proportion of DEGs from comparisons in (a) that overlap genes selectively expressed in aCMs at P0 and P28. We did not observe enrichment of P0 or P28 selective aCM genes in early or late pseudotime clusters, respectively. This suggested that pseudotime trajectories did not correspond to chronological time. f-g. GO biological process terms enriched for DEGs for the comparisons shown in (a). The top 10 terms enriched by genes upregulated in the indicated cluster are shown. Functional terms related to cardiomyocyte function were enriched in the late pseudotime clusters, Myo_1 (control) and Myo_6 (AKO). Two-tailed Fisher’s exact test, Bonferroni correction. h, WNN UMAP plot colored by a ‘functional cardiac gene’ index, which was calculated based on the aggregate expression of the six indicated genes, which are required for the efficient pumping function of aCMs.