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Figure 3 (A,B) Confocal images show dorsal CNCCs of the first two arches labeled by sox10:Dsred and pou3f3b:Gal4; UAS:nlsGFP in control and foxc1a–/–; foxc1b–/– mutant embryos at 48 hpf. Scale bar = 100 μm. (C,D) Confocal images show loss of dorsal cartilages in foxc1a–/–; foxc1b–/– mutant embryos at 6 dpf. sox10:Dsred+ cartilages are seen in single channels in C’ and D’, with dashed lines highlighting boundaries of dorsal arch and otic cartilage. (E) Peak intensity plots of Group I and Group II elements in control and foxc1a–/–; foxc1b–/– mutant embryos. Peaks above the dashed lines are reduced in mutants. (F,G) De novo motif enrichment of Foxc1-dependent and Foxc1-independent Group I and Group II elements. Top six motifs are shown with associated p-values after removing redundant motifs.