RNA-seq analysis of Per KO C2C12 cells. (A) Relative expression levels of Per1 and Per2 mRNAs in C2C12 cells after KD of each gene. The expression level with control scrambled shRNA was defined as 1.0 for each gene. ***, P < 0.001 with Student’s t test. Data are presented as mean + SEM of biological triplicates. (B) Indel frequency in Per1 KO and Per2 KO C2C12 cells analyzed with TIDE software (https://tide.nki.nl/). (C) Western blotting demonstrating down-regulation of Per1 and Per2 in KD and KO cells. Histone H2B was used as a loading control (Cont). (D) Venn diagrams displaying the number of genes whose expression levels were >200% or <50% of those of control KO cells. n = 1 in D–G. (E) The number of genes that were commonly up-regulated (> Cont × 2) or down-regulated (< Cont × 0.5) more than twofold in Per1 KO and Per2 KO cells compared with control KO cells. (F) Scatterplots comparing control, Per1 KO, and Per2 KO C2C12 cells. (G) Gene ontology (GO) terms relevant to muscle differentiation that were enriched in the genes commonly down-regulated in Per1 KO and Per2 KO cells compared with control KO cells. FC, fold change.