Fig 2: Representative enrichment of gene ontology among differentially expressed genes. (a) Gene ontology (GO) enrichment analysis on all differentially expressed genes due to knockdown of CHD8. (b) GO enrichment analysis on genes downregulated in response to knockdown of CHD8. Upregulated genes subjected to GO analysis indicated enrichment of mitochondrial membrane genes only (not shown). P-value represents Benjamini–Hotchberg correction for multiple tests. CHD8, chromodomain helicase DNA-binding protein 8.

Fig 3: Quantitative modeling of disruptive mutations in CHD8. (a) Quantitative PCR showed that a 20 nM concentration of CHD8 siRNA resulted in an ~50% reduction of CHD8 transcript. (b) Representative western blot indicated decreased CHD8 protein following CHD8 siRNA-mediated knockdown. (c) Quantitative analysis of western blot data shows a significant reduction in CHD8 protein following CHD8 siRNA treatment. Error bars are s.e.m., **P<0.01, *P<0.05. CHD8, chromodomain helicase DNA-binding protein 8; siRNA, small interfering RNA.

Fig 4: qPCR validation of differentially expressed genes identified by RNA-Seq. Fifteen genes excluding CHD8 were assayed via qPCR to establish the validity of the differential expression analysis based on the obtained RNA-seq data. qPCR and RNA-seq values showed a statistically significant correlation with both Pearson and Spearman methods. qPCR, quantitative PCR.