Genome-wide expression profiling in Drosophila wing imaginal discs

The imaginal discs of Drosophila melanogaster, where most known Hedgehog (Hh) signaling target genes are expressed with a restricted pattern, offers an accessible model system for identifying novel targets of the Hh signaling pathway. In the wing discs, cells near the A/P compartment boundary (B: ptc+) receive the highest level of Hh stimulation, A cells (A: hh-) further from the border receive lower levels of stimulation, while P cells (P: hh+) do not respond to Hh. To identify target genes whose expression is controlled by Hh signaling activity, we performed a systematic comparison of gene expression profiles among the A cells (A: hh-), the A cells adjacent to the A/P compartment boundary (B: ptc+), and P cells (P: hh+) via microarray analysis. For this study, 200 pairs of wing imaginal discs were dissected from third instar larvae of the genotypes w; UAS-mCD8GFP/+; hh-Gal4/+ or w; UAS-mCD8GFP/+; ptc-Gal4/+. The purpose was to separate and get the homogeneous populations of the cells have the different response to Hh stimulation in imaginal discs development. To this end, three part of cells [Anterior cells which receive low levels of Hh stimulation (A: hh-), Posterior cells which do not respond to Hh (P: hh+) , and the cells near the A/P compartment boundary which receive the highest level of Hh stimulation (B: ptc+), and ] were dissociated from tissue and sorted by FACS.