The cDNA library used to make the microarrays consists of 17,692 bovine cDNA samples, with 1,536 bovine ovary cDNA (Takasuga et al., 2001) and 16,156 bovine cDNA clones from USDA BOV1-5 libraries (including ovary) (Smith et al., 2001; Sonstegard et al., 2002), representing 15,634 unique genes. The cDNA inserts were amplified in 96-well PCR plates with M13 forward (5’-CCC AGT CAC GAC GTT GTA AAA CG) and reverse (5’-AGC GGA TAA CAA TTT CAC ACA GG) primers (IDT DNA, Coralville, IA). PCR products were visualized in 1% agarose gels using ethidium bromide staining. All products were then purified with 384-well MultiScreen PCR purification plates (Millipore, Billerica, MA). The purified DNA products were dried and stored at -80°C until used. Before printing, the dried PCR products were re-suspended in 3×SSC for 48 hours. Arrays were printed on poly-L-lysine (Sigma, St. Louis, MO) coated Gold Seal micro slides (Gold Seal Products, Portsmouth, NH) at the MU animal science microarray core. As external controls, the arrays also contained 10 Arabidopsis genes, each of them printed 10 times across the array (Spot report oligo, Stratagene, Cedar Creek, TX). Blank spots and 3× SSC were used as negative controls. A robotic microarray printer with 32 printing tips was used to spot the DNA. The bovine cDNA arrays had a total of 19,200 spots and were organized in 32 blocks arrayed in 8 rows and 4 columns. Each block had 600 spots arranged in 24 rows and 25 columns. Slides were stored in the dark until used.
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