The array image data (.CEL files) is processed by Model-based analysis of Tiling-array (MAT), to generate a binary file (.bar) that descrive MATscores of every probe on the array. Genomic location is derived from UCSC database (mm9). The resultant .bar file is converted into the txt file.
Genomic DNA digested by a methylation sensitive restriction enzyme, HpyCH4IV, are amplified by ligation mediated PCR.
Hybridization is carried-out using Hybridization oven 645 (Affymetrix) and GeneChip Fluidics Station 450 (Affymetrix) by according to the manufacture's instruction.
Microarray is sccaned using GeneChip 3000 7G Scanner with GCOS (v1.4) (Affymetrix)