Identification of genes whose expression is affected by ptc + dpp double RNAi in spider embryos

In the spider Parasteatoda tepidariorum, Hedgehog (Hh) and Decapentaplegic (Dpp) signaling play key roles in the formation of the two major embryonic axes (Akiyama-Oda and Oda, 2010, Development 137, 1263-1273; Akiyama-Oda and Oda, 2006, Development 133, 2347-2357). Patched (Ptc), a receptor for Hh,functions as a negative regulator of Hh signaling. Double parental RNA interference (pRNAi) against spider homologs of ptc and dpp, Pt-ptc and Pt-dpp, respectively, results in severe defects in axis formation. In this microarray experiment, we attempted to identify candidate genes whose expressions are regulated by Hh and Dpp signaling during axis formation. The objective of this experiment was a screen for genes whose expressions might be affected by Pt-ptc + Pt-dpp double pRNAi in spider embryos. Oligonucleotide probes were designed based on accumulated P. tepidariorum EST and cDNA sequences and embedded in custom microarrays (12K x2). Total RNA was extracted from late stage 5 embryos derived from a mated female before and after injection of dsRNA targeted for Pt-ptc and Pt-dpp. Gene expression levels were compared between the untreated (normal) and the Pt-ptc + Pt-dpp pRNAi-treated (pd-RNAi) samples. The same RNA sample was hybridized to the two different array platforms (GPL11390 and GPL11391).