Supplementary Figure 5: Chd8 RNA-seq and ChIP-seq analyses.
From: Germline Chd8 haploinsufficiency alters brain development in mouse
A. Results from RSAT de novo motif analysis on our Chd8 ChIP-seq peaks. Highlighted are three representative results for significant YY1, NRF1, and NFYB motifs (left), and corresponding predicted motif sites within Chd8 ChIP-seq peaks (middle) and the identified motif (right). B-C. Comparison of DE genes in our RNA-seq data with two recent Chd8 models, Katayama et al. (2016) (germline heterozygous Chd8), and Durak et al. (2016) (Chd8 knockdown). Dots represent genes passing FDR < 0.05 in our data and in either Katayama et al. (2016) or Durak et al. (2016) compared to our model (n = 37 and 77, respectively). The red dot indicates Chd8. DE genes in our data are significantly enriched in both datasets, but overlap between our data is stronger with Durak et al. (2016) than with Katayama et al. (2016). D. Differential expression of example synaptic genes. Top panels show expression (log2RPKM) across stages, bottom shows first four early developmental stages only. From left to right: Scn2b, Cacna1e, Cacna2d1, Cacna1b. Solid line = mean, dashed line = ±1 s.e.m. Black: WT; Red: Chd8+/del5.
