(A–B) Double fluorescent RNA in situ hybridization (FISH) for hh (magenta) and neuronal markers (A) pc2 or (B) chat (green) in wild-type animals. Main panels show cephalic ganglia. Lower panels show high magnification images of, from left to right, hh (magenta), pc2 or chat (green), DAPI (gray), and merged channels from a representative double-positive neuron. (C) Excision of cephalic ganglia tissue from acid-killed animals for RNA isolation. The left panel shows incision in the dorsal epidermis. Middle panel shows detail of the boxed region in the left panel after removal of dorsal epidermis. The right panel shows the detail of the boxed region in the middle panel after removal of gut tissue overlying the cephalic ganglia and ventral nerve cords. Abbreviations: inc, incision; gut, gut branches; phx, pharynx; CG, cephalic ganglia; VNC, ventral nerve cords. See methods for dissection protocol. (D) Representative image of amputation used to collect tissue for generating the head fragment Illumina libraries. Circle indicates the portion of the animal taken for RNA isolation. (E) Bar graph depicting log2 fold enrichment of selected markers in cephalic ganglia transcriptome over the head fragment transcriptome. Experimentally-verified neural markers and non-neural markers identified by brackets. Average log2 fold enrichment of all 7 CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 2.57. Average log2 fold depletion of all 22 non-CNS genes listed in Figure 1—source data 2 in cephalic ganglia transcriptome is 1.22. Statistically significant log2 fold change indicated by asterisks (*padj≤0.05, **padj≤0.001). For a list of all analyzed genes, see Figure 1—source data 1. (F) Bar graph depicting log2 fold enrichment of transcript expression level in the cephalic ganglia tissue of hh(RNAi) animals (blue bars) or ptc(RNAi) animals (red bars) over cephalic ganglia tissue from control(RNAi) animals. (G) Intersection of CNS-enriched genes (n = 2237) and Hh-dependent genes (n = 30) reveals 7 CNS genes misregulated following Hh pathway perturbation. Bar graph shows CNS enrichment (green bar) and relative expression following RNAi of hh (blue bar) or ptc (red bar) for if-1 and cali (*padj≤0.05, **padj≤ 0.01). (H–I) WISH for (H) if-1 and (I) cali. Dorsal surface shown on left, ventral surface shown on the right. Anterior up, maximum intensity projection of the ventral domain shown for A, B. Anterior up for H, I. Scale bars: 50 um for overviews, 10 um for insets for A, B; 500 um for H, I.