Table S1. Full averaged data. The average log2 expression value relative to the 0 hour for the dauer exit and L1 starvation time courses for all the genes. This table also contains the magnitude of difference between the minimum and maximum expression levels during the dauer exit and L1 feeding time courses. To analyze the time course data using magnitude of expression change, first download this table and sort by the preferred threshold. The difference between T0 and T12 in the dauer adjustment experiment is also included.

Table S2. All Raw data. This table contains the original normalized log2(expt/ref) expression ratio data downloaded from the Stanford Microarray Database for each gene. Additionally, this tables includes the P values that were calculated for the Student's t-test, one-way ANOVA and two-way mixed-model ANOVA comparisons for each gene.

Expression patterns of genes in mount 5 are heterogeneous. Hierarchical clustering was used to display the ratio of dauer to L1 at 0 hours (D/L1) and the expression ratios of the 1018 mount 5 genes during the dauer exit and L1 starvation time courses. Rows represent different genes and columns represent different times during the time course. At least two different expression profiles are evident in the genes of mount 5, as indicated by the light blue and purple bars on the right. Scale shows level of expression. D, dauer; L1, L1 larvae.

Expression patterns of genes in mount 22. Hierarchical clustering was used to display the ratio of dauer to L1 at 0 hours (D/L1) and the expression ratios of the 154 mount 22 genes during the dauer exit and L1 starvation time courses. In general the expression patterns for the genes in mount 22 are downregulated during dauer exit, as seen by the pattern of increasing blue intensity during the time course. This would suggest that the mount 22 genes are dauer enriched and is also reflected by the fact that mount 22 is over-represented in the dauer-enriched gene class. However, the majority of mount 22 gene expression patterns appear to be derived from contaminating carcasses. First, most of the genes in mount 22 are expressed less in dauers than in mixed-staged reference RNA, as indicated in column 3 (mostly blue). Second, data from the pure dauer population indicates that most genes are not significantly more expressed at 0 hours than at 12 hours after feeding of the pure dauers (column 2, few strong yellow). Rows represent different genes and columns represent different times during the time course. Scale shows level of expression. D, dauer; L1, L1 larvae.

Expression patterns of Hh-like genes. Hierarchical clustering was used to display the ratio of dauer to L1 at 0 hours (D/L1) and the expression ratios of the 43 Hh-like genes during the dauer exit and L1 starvation time courses. Rows represent different genes and columns represent different times during the time course. Scale shows level of expression. D, dauer; L1, L1 larvae.