total cellular RNA was isolated using RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, possible contamination by genomic DNA was removed by DNAseI treatment using the RNAse-Free DNAse Set (Qiagen), quality was checked by spectrophotometry and agarose gel electrophoresis, 2µg RNA per sample was used for cDNA preparation when A260:A280 ratio was 1.8-2.1 and RNA was intact
Raw data were analysed using Codelink Expression Analysis v.4.1 software to extract MDFCs (minimal detectable fold changes). Subsequent analysis was done using R and Bioconductor. Only probes with probe type „DISCOVERY“ and no MSR (Manufactory Slide Report) flag were used, leaving 19580 genes. Intensity values <0.01 were set to 0.01. Raw intensities were scaled to array median. After log2-transformation, quantile normalization was applied across all arrays.
