Transcriptome profiling of slr-2, C.elegans C2H2 Zn-finger

Our slr-2 dataset showed strong overrepresentation of genes previously identified in a serial analysis of gene expression (SAGE) intestinal library (McGhee et al., 2006) (p << 0.01); 812 genes were common to both data sets. Consistent with the deregulation of intestinal genes, we observed repression of several important metabolic pathways, including the TOR and insulin signaling networks, suggesting that slr-2(ku297) mutants experience metabolic stress. We also compared differentially regulated genes in slr-2 and lin-35 single mutants. Again, we saw a statistically significant overlap (p-value < 0.01); 261 genes were present in both data sets. Strikingly, > 75% of genes common both datasets showed expression changes in the same direction, although the common dataset contained an approximately equal mixture of up and downregulated genes. Furthermore, more than fifty genes common to the lin-35 and slr-2 datasets are known to have intestinal-associated functions. That some of these common intestinal genes were absent from the gut SAGE library could be due to differences in the developmental stage of the animals assayed (adults versus L1s) as well as experimental approaches (SAGE versus microarrays) Keywords: analysis of staged mutant worms We compared transcriptome profiles of slr-2 mutants and control N2 worms at L1 stage stage. Each comparison was done in triplicate with independently grown and isolated animals. Data for N2 L1 stage were from our previous experiments (Series GSE6547) To achieve higher accuracy, RMA values were calculated on the basis of 21 microarray experiments (including data from Series GSE6547)