Gene Expression Profiling of Pigs

cDNA was prepared from total RNA by standard methods. Gene expression experiments were conducted on custom Sus Scrofa 12-plex microarrays containing 142 073 probes targeting 17 261 genes. Probe selection and array design is described elsewhere.^{59 (link)} In all, 200 ng double-stranded cDNA was Cy3-labelled using the 'One colour DNA Labelling Kit' (Roche NimbleGen, Madison, WI, USA). A minimum of three technical replicates of each sample were loaded, and raw data intensities were collected using a NimbleGen MS200 scanner. Background corrected, quantile normalised and RMA (Robust Multi-Array Analysis) normalised probe intensities were generated using the NimbleScan v2.6 software (Roche NimbleGen). Average signal intensities were calculated for each probe set and log2 transformed. Data were analysed using the Partek Genomics Suite software, v6.6 (Partek, St Louis, MO, USA). Significant differentially expressed genes were identified for a false-discovery rate P-value of 0.05 and twofold change.