Gene expression

(a) Expression Heatmap. A heatmap of sample-to-sample distances on the matrix of variance stabilized data for overall gene expression is shown where darker red colors indicate more similar expression, as shown on the color key to the upper right of the panel. Clustering, drawn above the heatmap, demonstrates that the adult samples are very similar to each other, but show complete separation from the embryonic samples. (b) Differential expression. Plot of differential gene expression with fold difference of log_{2} normalized expression in adult cerebral cortex (*n*=3) versus embryonic cerebral cortex (*n*=4) on the x-axis and −log_{10} adjusted *p*-value on the y-axis. Each gene is colored based on the log_{10} base mean expression, i.e. more highly expressed genes are in darker colors. (c) Technical validation of differential expression. The x-axis shows the log_{2} fold expression (Adult/Embryonic) using the RNA-Seq data compared to qRT-PCR data for eight genes (y axis). *Ppid* was used as the normalization gene. The size of each point represents the base mean expression level from the RNA-Seq data as in (b). The grey shaded area indicates the 95% confidence interval for the regression. (d) Boxplots showing biological validation of differential expression. The same eight genes were used for validation with a new set of animals and an expanded set of developmental stages. On the y-axes are the log_{2} expression values normalized to E15 measured with qRT-PCR with *Ppid* used as the normalization gene. The x-axes show each developmental stage with E15 (*n*=4), E17 (*n*=5), P0 (*n*=6), P14 (*n*=4), P28 (*n*=4), and adult (*n*=4). The boxes represent the range between first and third quartiles and whiskers indicate highest value and lowest values within 1.5 multiples of the inter-quartile range; outliers from this range are plotted as individual dots.

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