1% SDS, 1% BSA) and 10 μl of formamide. Probes
were denatured at 95°C for 5 min and applied onto the genomic array slide, covered with a cover slip (Hybri-slips, Sigma-Aldrich Co. St Louis U.S.A.) and hybridized at 45°C for 16 h. After hybridization the slides were washed sequentially for 5 min each in 2× SSC-0.1% SDS, 0.1× SSC-0.1% SDS, 0.1× SSC, and Ibrutinib concentration 0.01× SSC. The slides were dried and fluorescent signals were scanned using an Axon Genepix 4000B scanner at a resolution of 10 μm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Each microarray experiment was repeated six times (two technical replicates with the same RNA samples and three biological replicates using RNA isolated from a different culture). Analysis of DNA microarray data Spot intensities www.selleckchem.com/products/BKM-120.html were quantified using Axon GenePix Pro 6.0 image analysis software. First, an automatic spot finding and quantification option of the software was used. Subsequently, all spots were inspected individually and in some cases, the spot diameters were corrected or the spots were removed from the analysis. The mean of the signals and the median of backgrounds were used for further analysis. Raw data were imported into the R 2.2.1 software [65]. Background signals were subtracted using the Robust Multichip Analysis “”RMA”" [66] whereas normalization of the signal intensities within slides was
carried out using the “”printtiploess”" Org 27569 method and the LIMMA package [67, 68]. Normalized data were log2 transformed and then fitted into mixed model ANOVAs using the Mixed procedure [17, 18]. The p-values of the bean extract effects were adjusted for by the False Discovery Rate method “”FDR”" [69]. Changes in signal intensity of ± 1.5-fold
or higher/lower between treatments and controls were highly significant (FDR, p-value ≤ 0.05), however we focus only in differential expressed genes that fall in the more traditional criteria, which is the cut-off threshold for up-regulated (≥ 2) and down-regulated genes (≤ 0.5). The genes were subject to cluster analysis with Gene Cluster 3.0, using the uncentered Pearson correlation and complete linkage clustering. Results were visualized with Treeview as described by Eisen and collaborators [18]. Microarray validation by Reverse transcription-PCR analysis RT-PCR analysis was carried out to validate the array hybridization data. RT-PCR analysis was performed for nine up-regulated genes under the effect of bean leaf extract. These RT-PCR experiments involved independent biological experiments from those used for microarray analysis. DNA-free RNA was obtained and checked for integrity in an agarose gel, 200 ng of total RNA were used for reverse transcription (RT) and PCR using the SuperScript one-step kit (Invitrogen, California, USA). A list of the primers used in this analysis is available on request.