Comparing the gene expression profile between wildtype and gal80? mutant of S. cerevisiae in fructose and fructose-palatinose mixture

We wanted to find out (1) which genes are affected by the active Gal4 in the gal80? mutant in fructose, and (2) which MAL genes are affected by the active Gal4 in the fructose-palatinose mixture. Overall design: 36-sample RNA-seq of three timepoints (fructose mid-log, 10h after mid-log and 16h after mid-log), two strains (wildtype & gal80?) and two conditions (0.1% fructose & 0.1%fructose+0.9% palatinose), in three biological replicates. The timepoints are chosen such that 10h after mid-log, fructose is running out; 16h after the mid-log, wildtype cells have highly activated MAL genes. The conditions are chosen because (1) 0.1% fructose does not repress the expression of GAL or MAL genes; (2) the growth rate of the wildtype and gal80? are similar in 0.1% fructose.