Tissue samples were gathered from consenting patients at the time of diagnostic procedures or at primary curative surgical resection at Galway University Hospital, Ireland. The cohort comprised of 101 colorectal tumour specimens, 8 TWS119 research buy polyps and 107 TAN tissues. Following retrieval, all samples were subject to

histopathological review prior immediate snap-freezing in liquid nitrogen and archival at -80 °C until further use. Concomitant clinicopathological data on patients and specimens was obtained through patient interview and review of clinical notes. Inhibitors,research,lifescience,medical Ethical approval for this study was granted by the Clinical Research Ethics Committee, Galway University Hospitals. Table 2 Clinico-pathological data for patients used for gene expression analysis RNA extraction and analysis Tissue Inhibitors,research,lifescience,medical samples (50-100 mg) were homogenised using a hand-held homogenizer (Polytron PT1600E) in 1-2 mL of QIAzol reagent

(Qiagen) as described previously (32). In brief, tumour and TAN samples were homogenised separately but on the same day. RNA was extracted using RNeasy Plus Mini kits (Qiagen) according to the manufacturer’s instructions. RNA was eluted in 60 µL volumes and stored at -80 °C. RNA concentration and purity was assessed in duplicate samples using a using a NanoDrop ND-1000 Inhibitors,research,lifescience,medical spectrophotometer (NanoDrop). RNA integrity was evaluated using the RNA 6000 Nano Chip kit (Series II) and the Agilent 2100 Bioanalyzer (Agilent Technologies). An RNA integrity number (RIN) was generated for each sample using the Agilent 2100 Expert Software (Version B.02.03) based on the ratio of ribosomal

bands and also the presence or absence of degradation products on the electrophoretic and gel-like images. A threshold value Inhibitors,research,lifescience,medical of RIN ≥7 was applied and RNA purity was verified by an average A260/A280 ratio of 1.98 (range, 1.97-2.01) and A260/A230 ration of 1.7 (range, 1.5-1.83). Reverse transcription RNA was reverse transcribed to first strand cDNA using Superscript III reverse transcriptase (Invitrogen) and random primers (N9; 1 µg, MWG Eurofins). Negative control samples were included in each set of reactions. Inhibitors,research,lifescience,medical Reactions were incubated at 25 °C for 5 minutes followed by 50 °C for 1 hour and final denaturation at 72 °C for 15 minutes. Samples were subsequently diluted to 100 µL in nuclease-free water and stored at -20 °C. Real-time quantitative PCR Amplification efficiency The amplification efficiency of each assay is an important consideration in the Chlormezanone determination of relative quantities of gene expression by RQ-PCR. PCR efficiency impacts greatly on the accuracy of the calculated expression result and is influenced by PCR reaction components. For 100% efficiency a doubling of the amount of DNA will occur at each cycle, while for 80% and 70% the amount of DNA will increase from 1 to 1.8 and 1.7, respectively. Resultantly, small differences in efficiency can greatly affect the calculation parameters involved in the determination of gene expression values.