Nimblegen porcine genome expression array

The RNA samples were sent to KangChen Bio-tech, China, for microarray hybridization. Each RNA sample from different PAM treatments was hybridized to one Roche NimbleGen Porcine Genome Expression Array (Roche). Briefly, double-stranded cDNA was synthesized from 6 mg of total RNA using a T7-oligo (dT) primer. The cDNA was further purified and converted into cRNA using an in vitro transcription reaction. Five mg cRNA was reverse transcribed to cDNA, fragmented, and then labeled with Cy3-dCTP (GE Healthcare) using Klenow. These labeled cDNA fragments were hybridized to NimbleGen Porcine Genome Expression Arrays for 16 h at 42°C using the Roche NimbleGen Hybridization System. Afterwards, the GeneChips were washed, stained, and then scanned with a Roche-NimbleGen MS200. The Roche NimbleGen Porcine Genome Expression Array contains over 135,000 probe sets, representing 45,023 transcripts and variants of pig from the database of RefSeq, Unigene and TIGR.