Fig. 2
Identification of Etv6 direct transcriptional targets in the somites. a Experimental design. RNA-seq was performed on wild type (WT) and Etv6-deficient (etv6 MO-injected embryos) somite explants dissected from stage 22 embryos. Differentially expressed genes (DEGs) were identified by comparing the transcriptome of these tissues. b Spearman correlation analysis on triple biological RNA-seq replicates. c MA plot (magnitude of the difference versus amplitude of the signal) showing the fold-change in gene expression of all genes in WT versus Etv6-deficient somites (log2FC) compared to their expression levels (log2CPM). Black dots, non-significant change; red dots, differentially expressed genes (DEGs). The number of positively and negatively regulated DEGs is indicated. d WISH showing the expression of DEGs in stage 22 WT and Etv6-deficient embryos. Meox2 expression is upregulated in the somites (arrows) in Etv6-deficient embryos whereas expression of crim1, sox18 and vegfa is downregulated. Note that vegfa expression in the hypochord is unaffected (arrowheads). Embryos are shown in lateral view with anterior to the left and dorsal to the top. Numbers in top right corner indicate the number of embryos exhibiting the phenotype pictured (scale bars: 0.5 mm). e The intersection between DEGs and genes harbouring Etv6 ChIP-seq peaks in their TSS region reveals 540 putative direct target genes. f Foxo3 and klf4 (arrows), known transcriptional regulators of vegfa, are amongst the 18 TFs and chromatin modifiers identified as potential direct transcriptional targets of Etv6
