The differentially expressed genes indentified by microarray were used to find pathways up- and down-regulated in the different tissues. The total RNA samples used for the

microarray analysis were also used for validation of the microarray results by quantitative RT-PCR (qPCR). cDNA synthesis for qPCR was performed using QScript (Quanta Biosciences) using 100 ng total RNA in 10 μl final selleck compound reaction volume according to the manufacturer’s instructions. A tissue specific RNA sample was made for each of the five tissues by mixing 1 μl total RNA from all samples within a tissue. From each of the tissue specific RNA samples a negative RT control was made by excluding the RT enzyme in the cDNA synthesis. An experiment wide RNA pool was made by mixing 2 μl from each of the tissue specific RNA samples together. The experiment wide RNA pool was used to make a dilution series with

250, 125, 62, and 31 ng RNA in the cDNA synthesis which was used to evaluate assay efficiency and linearity. After cDNA synthesis all cDNA samples were diluted 1:10 in water and stored at − 20 °C until analyzed. qPCR analysis was carried out in 384 well plates on Applied Biosystems 7900HT real time instrument. Regorafenib A semi-fast cycling protocol was used, consisting of 3 min denaturation at 95 °C followed by 40 cycles of 5 s at 95 °C and 15 s at 60 °C. All amplifications were run in 5 μl volume with 1.5 μl cDNA, 900 nM of each primer and 200 nM probe and 2 × Briliant III Ultra-Fast QPCR Master Mix (Agilent Technologies). ROX was added to a final concentration of 300 nM as a passive reference dye. Eight different assays were run on each plate, always including the assay for elongation factor 1α

filipin (EF1α). In addition “No Template Control” (NTC; water), − RT from all tissues and the dilution series were included for all assays. Data were analyzed using SDS 2.4 and RQ Manager 1.2.1, with baseline and threshold for Cq values set manually for each gene and kept identical for all plates. Data were further analyzed in R (http://www.R-project.org). Relative quantification of gene expression was carried out according to the ΔΔCt method (Livak and Schmittgen, 2001), using normalized RNA template amounts (thus omitting an endogenous standard gene) and ovary as calibrator tissue. To validate the microarray data, a gene specific qPCR analysis was performed on 12 genes with probes on the microarray. All genes were analyzed for each of the five tissues, and the relative transcription compared to the corresponding probe intensities from the microarray analysis. All assays demonstrated a high level of correlation between the qPCR and microarray result in all five tissues, confirming the microarray results (Fig. 2 and Supplementary Fig. 1).