Genomic DNA (250 ng) is digested by NspI and amplified using a ligation-mediated PCR with adapters covalently linked to the restriction fragments. In the next step PCR products are purified using magnetic beads, fragmented using DNase I, labeling with biotin and hybridized overnight (16–18 h) to a 49-format array. After incubation samples are washed and stained with streptavidin using a GeneChip Fluidics Station 450. Finally, arrays are scanned by GeneChip Scanner 3000, using the GeneChip Command Console Software (Thermo Fisher Scientific), to generate the CEL files that includes the intensity probe signals.