RNA microarray analysis

To measure fluctuations in gene expression, Affymetrix genechips (GeneChip Yeast Genome 2.0 Array) were utilized. These Gene Chips provide comprehensive coverage of both S. cerevisiae (5,841 probe sets) and Schizosaccharomyces pombe (5,021 probe sets). Total RNA extracted from Sc57-Te₅^R strain treated with K₂TeO₃ and from an untreated control was used to prepare molecular probes. Three independent RNA extractions were performed on each single yeast sample. Probe preparation and microarray hybridization were performed in the laboratory of the University of Bristol, following manufacturer’s instructions. Microarray data were analyzed using the FlexArray 1.6.1 software suite (Génome Québec and McGill University). Raw data were normalized using the PLIER (Probe Logarithmic Intensity Error) algorithm. This algorithm is the latest in a series of algorithms produced by Affymetrix to analyze their oligonucleotide GeneChips and employs M-estimators to obtain estimates of probe affinity and target signal. Significant expression differences were identified by means of t-tests. Only differently expressed sequences with p-values < 0.01 and expression ratios >2.0 were taken into consideration. Differential gene expression was assessed using «The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8» (https://david.ncifcrf.gov/), in order to enrich the data obtained and deduce groups of genes with altered expression values due to the applied treatment.