To disrupt each sample of tissue we added 400 μl of cell disruption buffer and then homogenized the sample with a motorized rotorstator. Total RNA was isolated from tissue samples using the mirVanaTMParisTM kit (Ambion/Applied Biosystems). The RNA obtained from each sample was then quantified by NanoDrop. Pools of three tissue samples in each were analysed using a final concentration of 50 ng/μl. A total of 3 μl of the small Selleckchem Protease Inhibitor Library RNA fraction were reverse-transcribed using the miRNA Megaplex reverse

transcription primers (for pools A and B) and the TaqMan® microRNA reverse transcription kit (both from Applied Biosystems). The cDNA obtained was amplified using TaqMan® PreAmp Master Mix and Megaplex PreAmp Primers (for pools A and B). For the reverse transcription of cel-miR-39, we prepared a reaction with RT master mix using the TaqMan® microRNA reverse transcription kit, cel-miR-39 RT primer (TaqMan MicroRNA assay) and total RNA. The reaction was incubated at 16°C for 30 min, followed by 42°C for 30 min and then 85°C for 5 min. An initial reverse CHIR-99021 cost transcription–quantitative polymerase chain

reaction (RT–qPCR) was performed to test the quality of cDNA before the definitive analysis. At this point, three types of quality control were used. Cel-miR-39 was used as a spiked-in control in serum samples. RNU48 was used to test the quality and integrity of the obtained cDNA tissue. Mammalian U6 (U6) was used in both types of samples (serum and tissue).

Ct values of 16–19 in serum samples and 15–18 in tissue samples were considered as valid. Each RT reaction was performed using TaqMan® 2× Universal PCR Master Mix, No AmpErase UNG (Applied Biosystems). Up to 700 miRNAs were evaluated by the TaqMan® human miRNA array. A TaqMan® human microRNA array card is a high-throughput PCR-based miRNA array that enables analysis of more than 700 miRNA assays on a microfluidic card. Simultaneous synthesis of cDNA for mature miRNAs was performed using Megaplex reverse transcription human pool A and B (Applied Biosystems). Each of these, EGFR inhibitor A and B, is a set of predefined pools of 384 stem-looped reverse transcription primers. RT–qPCR was performed using the Applied Biosystems 7900HT fast real-time PCR system and default thermal-cycling conditions. Data analysis was performed using Expression Suite software (Applied Biosystems) and the HTqPCR library in r [27]. The ΔCt values were obtained using the mean expression value of all expressed miRNAs in a given sample as a normalization factor for miRNA RT–qPCR data, according to the procedure described by Mestdagh et al. [28]. The results were expressed as log2 fold change from ΔCt values. We discarded fold change values between −2 and 2 in absolute terms, with mean values between −1 and 1 expressed as log2 fold change.