Fig 1: The Gene Set Jointly Regulated by Six3 and Six6 Highly Overlaps with the Gene Networks Regulated by WNT3A, CTNNB1, POU4F2, or SOX2(A) RNA-seq not only confirmed most known DEGs but also identified additional DEGs, e.g., Fzd1, Wnt3a, Cdon, and Wnt16, in DKO retinas. Normalized counts generated using DESeq2 were used for plotting. The DEGs are in Table S2.(B) The gene set jointly regulated by Six3 and Six6 highly overlapped with the GRNs regulated by WNT3A, CTNNB1, POU4F2, or SOX2, which were among the top five upstream regulators in IPA. The predicted functions of DEGs matched the observed phenotypes.(C–N) Fzd1 (C–F), Wnt3a (G–J), and Wnt16 (K–N) were upregulated in E14.5 DKO retinas (F, J, and N) compared to those in Six3F/F;Six6+/− retinas (C, G, and K), Six3F/F;Six6−/− retinas (D, H, and L), and Six3F/F;α-Cre retinas (E, I, and M). Six3 deletion was shown in Figures 2A–2D.Scale bar, 100 μm (C). n = 3 embryos