Total RNA (5 μg) with oligo(dT)20 and dNTP mix was incubated at 65°C for 5 min

and cooled on ice for 1 min. For each total RNA sample, 10 μl cDNA synthesis mix was made: 10× RT buffer, 25 mM MgCl2, 0.1 M DTT, 40 U/μl RNaseOUT and 200 U/μl Superscript III RT. The samples were mixed gently and collected by brief centrifugation. Then, the samples were incubated in a thermal cycler at 42°C for 50 min and the reaction was terminated at 70°C for 15 min and cooled on ice. Finally, the reactions were collected by brief centrifugation, and 1 μl of RNase H was added to each sample and incubated for 20 min at 37°C. The cDNA prepared was used for real-time PCR. DNA Temozolomide solubility dmso microarray The 32P-labeled cDNA probes were prepared using the Atlas Pure Total RNA Labeling System (Clontech Laboratories)

as previously described [46]. This array was the only one available commercially when the experiments were performed. In brief, 5 μg of total RNA was reverse transcribed using the primer mix supplied with each array. The mixture was heated to 65°C for 2 min in Erlotinib concentration a PCR thermal cycler, followed by 50°C for 2 min in presence of a master mix containing 5× Reaction buffer, dNTP, and dATP. The DTT and MMLV reverse transcriptase was added, mixed and incubated for 25 min at 50°C. Then, 10× termination mix was added to end the reaction. Unincorporated nucleotides were removed using a Nucleospin Extraction Spin Column (Clontech Laboratories, Palo Alto, CA) as per the manufacturer’s instructions. Scintillation counting was done to measure the incorporation Chorioepithelioma of radionucleotide into the probe. The Clontech Human Nylon Filter Arrays (Clontech Laboratories), containing DNA sequences for 1,500

genes, were prehybridized in 5 ml of Express-Hyb solution supplemented with 0.5 mg salmon testes DNA at 68°C for 30 min. The radiolabeled cDNA probe was heated in a boiling water bath for 2 min, followed by 2 min on ice. Then it was added to the hybridization solution and allowed to hybridize to the filter array overnight. The membranes were washed in SSC plus 0.1% sodium dodecyl sulphate (SDS) at 68°C for 30 min and further rinsed in SSC for 5 min at room temperature. Next, the filters were wrapped in plastic wrap and exposed to a phosphor imaging screen for 24 h. Analysis of the phosphor imaging screens was done by using a phosphor imager (Perkin Elmer, Boston, MA) and AtlasImage 2.0 software. Global normalization method was used, by the background subtraction method followed by SAM analysis. For most of the genes, a Q value (percent change that the gene is false-positive) of 5% was used as the cut-off value. The quality of the hybridization signals was assessed using scatter plot analysis of replicate samples, as well as by calculating the coefficient of variance. Only samples with hybridizations with high correlation levels (p > 0.9) among replicates were used for subsequent analysis.