Fig. 3
Gene expression changes in Chd8-deficient neocortices. a Volcano plot indicating all DEGs detected by DESeq2 in E12.5 Chd8+/− embryonic cortices. Each point represents an individual gene, and all heterozygote DEGs (FDR < 0.05) are highlighted in red. n = 3 per condition. b Volcano plot showing all DESeq2 detected DEGs in E12.5 neo/neo cortex. All differentially expressed genes (FDR < 0.05) are highlighted in red. n = 3 per condition. c Volcano plot of all DESeq2 detected DEGs in E12.5 neo/− cortex. All differentially expressed genes (FDR < 0.05) are highlighted in red. n = 3 per condition. d Heatmap of genes differentially expressed in neo/neo and neo/− embryos, indicating transformed relative expression levels in +/+, +/−, neo/neo and neo/− embryos. e Mean normalised count of aligned RNA-seq reads for a selection of genes that were differentially expressed in the mild and severe hypomorphs. f Venn diagram showing extent of overlap between neo/neo and neo/− DEGs and ASD associated genes obtained from the SFARI Human Gene database (https://gene.sfari.org/autdb/HG_Home.do, accessed March 2018). g Breakdown of neo/neo and neo/− DEGs that are ASD associated, DEGs with known CHD8 binding sites in E17.5 mouse neocortex, human mid foetal cortex and NSCs; and DEGs that are both ASD associated and have known CHD8 binding sites. Downregulated genes are denoted by a negative number. h Breakdown of neo/neo and neo/− DEGs with H3K27me3 in neural progenitors, DEGs with known REST binding sites, and DEGs that have been shown to have both H3K27me3 in neural progenitors and REST binding sites. Downregulated genes are denoted by a negative number. i Gene Ontology (GO) analysis of up and down-regulated neo/neo and neo/− DEGs under the “Biological Processes” category. The five most significant hits are shown for each set. See also Additional file 4: Table S3