The hybridization was carried out using the 3DNA Array 350 kit (Genisphere Inc., Hatfield, PA) according to the manufacture?s instructions. For each hybridization, 5?g of total RNA of each follicle sample were used. After hybridization, the slides were scanned using an Axon GenePix 4000B scanner (Axon Instruments Inc., Union City, CA) at 5?m resolution, and the image was analyzed using GenePix Pro 4.0.1.12 software (Axon Instruments Inc., Union City, CA). The result files and the image were linked together and stored in the local BioArray Software Environment (BASE) database (Saal et al., 2002).
Data processing
The result data were first filtered to remove all control spots, 3× SSC, and blank spots. Then the background-corrected-median-intensities were normalized using a pin-based-lowess-normalization within BASE. The log ratio of chanel 1 VS. chanel 2 were then outputed together with the raw data for each spot of all the arrays.
