Fig. 7

RNAseq transcriptome analysis identifies a role for alx1 and alx3 in oxidative stress response regulation.alx1^uw2016;Tg(sox10:kaede) embryos were injected with alx3 CRISPR RNPs to induce somatic mutations at the alx3 locus to generate alx1;alx3CR embryos. At 3 dpf,alx1;alx3CR embryos with characteristic craniofacial defects and age-matched Tg(sox10:kaede) embryos were lysed. A total of six replicate groups of 20 embryos from each genotype were collected in two independent experiments for RNA extraction and Illumina high-throughput sequencing. (A) Volcano plot shows the distribution of genes that are differentially expressed in alx1;alx3CR;sox10:GFP embryos relative to sox10:GFP embryos at 3 dpf. Vertical lines indicate −1.5-fold and +1.5-fold change cut-offs, and the horizontal line indicates the FDR=0.05 cutoff. (B,C) molecular pathways that are significantly suppressed (B) or activated (C) in alx1;alx3CR;sox10:GFP embryos were identified using GSEA, with top 20 activated and top 20 suppressed terms shown as a 2D map to emphasize overlaps. (D) Heatmap summary of differentially expressed oxidative stress response genes shows increased expression levels of these genes in alx1;alx3CR;sox10:GFP embryos.