Project description:Technological advances now make gene expression analysis feasible in any sequenced organism, and new sequencing methods have greatly accelerated genome sequencing. Here we show that important insights into gene function are possible by comparing gene expression response to genetic and environmental perturbations between related species. We present a gene expression compendium designed for maximal gene expression variation in the sensu stricto yeast Saccharomyces bayanus. While many aspects of gene expression are conserved over the 20 million years of evolution separating S. bayanus from the model yeast S. cerevisiae, we observe regulatory changes, including in galactose metabolism and sporulation. The expression data also allows us to predict the biological roles of genes unique to S. bayanus, leading us to propose a role in oxidative stress response for a group of genes, and also to identify a regulatory network specific to this yeast. This dataset contains 53 experiments as follows: (experiment: number of datasets (number of arrays)) growth at different temperatures: 1 (3) heat shock: 4 (18) ammonium: 1 (6) cadmium: 1 (4) copper: 1 (6) lead: 1 (6) nickel: 1 (5) sulfite toxicity: 1 (6) zinc: 1 (6) ethanol toxicity: 1 (6) sorbitol: 1 (6) bleach: 1 (6) hydrogen peroxide: 3 (17) 2-deoxyglucose: 1 (6) hydroxyurea: 1 (6) lovastatin: 1 (4) MG-132: 1 (5) MMS: 1 (6) rapamycin: 1 (6) tunicamycin: 1 (6) zeocin: 1 (6) chronological aging: 3 (13) diauxic shift: 1 (6) galactose: 5 (38) glycerol: 1 (4) sucrose: 1 (4) auxotroph starvation: 1 (11) nutrient limited chemostat growth: 3 (7) mating type and ploidy: 1 (3) alpha factor: 1 (8) cell cycle: 1 (30) sporulation: 3 (18) strain backgrounds: 1 (4) cross progeny: 1 (22) Tn7 insertions: 1 (27) 555.11 and 670.20 knockout tetrads: 2 (8) Timecourse datasets: heat shock, ammonium, cadmium, copper, lead, nickel, sulfite toxicity, zinc, ethanol toxicity, sorbitol, bleach, hydrogen peroxide, 2-deoxyglucose, hydroxyurea, lovastatin, MG-132, MMS, rapamycin, tunicamycin, zeocin, chronological aging, diauxic shift, galactose, glycerol, sucrose, auxotroph starvation, alpha factor, cell cycle, sporulation Single timepoint datasets: growth at different temperatures, strain backgrounds, cross progeny, Tn7 insertions, nutrient limited chemostat growth, mating type and ploidy, 555.11 and 670.20 knockout tetrads Almost all samples were hybridized versus a common reference prepared from a mixture of RNA from Mat a, Matx, and Mata/x cells sampled in both exponential and stationary phase. Additionally, RNA from stress conditions was included: hydrogen peroxide treatment sampled at 10, 30 and 45 minutes, and heat shock from 25 to 37 degrees sampled at 10 and 30 minutes. Samples from the following datasets were not hybridized versus the common reference (reference used in parenthesis and in array annotations): cell cycle (asynchronous culture), constant temperatures (log phase culture), mating type and ploidy (log phase culture), diauxic shift (log phase culture), and strain backgrounds (log phase culture). Replicates and dye swaps were not used.
2010-05-16 | E-GEOD-16544 | biostudies-arrayexpress
