BioProject

RNA was isolated from Upf225G/Y; Btl-GAL4, UAS-GFP/+ and y w FRT19A/ Y; Btl-GAL4, UAS-GFP/+ L3 larvae using Trizol as described in Materials and Methods, cDNA labeled with Cy3 or Cy5 was prepared from each RNA sample and hybridized to microarrays containing ~14,000 gene probes covering the entire Drosophila genome (Gerber et al. More...

RNA was isolated from Upf225G/Y; Btl-GAL4, UAS-GFP/+ and y w FRT19A/ Y; Btl-GAL4, UAS-GFP/+ L3 larvae using Trizol as described in Materials and Methods, cDNA labeled with Cy3 or Cy5 was prepared from each RNA sample and hybridized to microarrays containing ~14,000 gene probes covering the entire Drosophila genome (Gerber et al. 2006). Hybridizations were performed with two independently isolated and labeled RNA samples. Analysis was carried out using the Stanford Microarray Database (http://genome-www5.stanford.edu/ ). During analysis we noted that the Upf225G mutants were delayed in development. To avoid confounding effects of changes in gene expression that result from developmental regulation rather than more direct effects of Upf2 loss of function, we used the available wild- type developmental gene expression time course (Arbeitman et al. 2002) to filter out genes whose transcription changes more than 25% from their maximal value during 72-96 hrs of larval development. The wild-type data set includes ~33% of genes, and we used just this subset for our analysis. Furthermore, the wild-type data set is for mixed sex populations, while our microarray was performed only on males. To compensate for sex differences, we also excluded from analysis genes that differed between males and females by more than 50% based on data from male and female larvae (E. Johnson and M.A.K., unpublished). Our analysis of genes regulated by NMD is therefore conservative, covering only non-developmentally regulated and non-sex regulated genes whose expression was affected by a hypomorphic Upf2 allele, and thus provides only a lower estimate on genes regulated by NMD. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Overall design: Computed Less...