C. elegans fer-1 mutant gene expression profile

In vertebrate muscle, loss of Dysferlin results in the activation of compensatory muscle gene expression, even at pre-pathological stages. We hypothesized that if C. elegans fer-1 is also expressed in muscle, then fer-1 mutant worms might also exhibit compensatory muscle gene expression. To test this hypothesis, we used Affymetrix microarrays to profile gene expression from synchronized wild type and fer-1 mutant adults. To improve the specificity of this approach, we profiled two well characterized loss-of-function fer-1 mutants (hc1ts and hc24ts) and considered genes that changed similarly in both mutants as fer-1-regulated transcripts. For each genotype, six individual replicates were performed and were hybridized to Affymetrix C. elegans Genechips using the manufacturer’s recommended protocols. The best four preparations (as determined by the overall Pearson Correlation within a genotype) were used for RNA labeling and hybridization.