RNA-sequencing analysis of <i>Phf6</i>-deleted and control E15.5 cortex and E16.5 cultured cortical neurons.

<p>(A) Multidimensional scaling (MDS) plot of N = 5 <i>Phf6</i><sup><i>–/Y</i></sup> <i>vs</i>. 3 <i>Phf6</i><sup><i>+/Y</i></sup> E15.5 cortices samples used for RNA-sequencing analysis, showing clustering of samples after adjustment for litter-effect; color-coded by genotype. (B) MDS plot of N = 4 <i>Phf6</i><sup><i>lox/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> vs. 3 <i>Phf6</i><sup><i>+/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> E16.5 cortical neuron isolates used for RNA-sequencing analysis showing clustering of samples after adjustment for litter-effect; color-coded by genotype. (C,D) Mean-difference plot for <i>Phf6</i><sup><i>–/Y</i></sup> <i>vs</i>. <i>Phf6</i><sup><i>+/Y</i></sup> E15.5 cortex RNA-sequencing data showing log<sub>2</sub>-fold change for each gene over average log<sub>2</sub> expression (C). Mean-difference plot for <i>Phf6</i><sup><i>lox/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> vs. <i>Phf6</i><sup><i>+/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> E16.5 cultured cortical neuron RNA-sequencing data (D). Significantly up- and downregulated genes in the <i>Phf6</i> deleted samples relative to controls are coloured red and blue respectively. NS = not significant. (E) Log<sub>2</sub> fold-change in RNA levels of ZIC family transcription factor genes in E15.5 <i>Phf6</i><sup><i>–/Y</i></sup> <i>vs</i>. <i>Phf6</i><sup><i>+/Y</i></sup> cortex. (F) Log<sub>2</sub> fold-change in RNA levels of the <i>Usp18</i> gene in <i>Phf6</i><sup><i>lox/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> vs. <i>Phf6</i><sup><i>+/Y</i></sup><i>;Nes-cre</i><sup><i>Tg/+</i></sup> E16.5 cortical neurons. RNA sequencing data were analysed as described in the methods section.</p> <p>(PDF)</p>