array scanning and feature extraction protocol
Slides were washed according to the manufacturer instrucutions (1 min buffer 1, 1 min buffer 2, dried in acetonitrile). Slides were scanned at 532 nm (Cy3) and 636 nm (Cy5). Parameters: Scanning hardware = Axon- GenePix4000B, Scanning software = GenePix Pro [Axon Instruments]
nucleic acid extraction protocol
DNA was extraction prior to labeling.
Grow 50ml of cell culture at 25C in rich media (YES) to OD600=0.3 (total OD=15) with or without 1 hour of growth at 36C. Cross-link for 30 min with 1% final concentration of 37% formaldehyde (1.35ml per sample). Add 2.5ml of 2.5M glycine and incubate for 10min. Pellet cells at 3000rpm and wash the pellet once with ice-cold PBS or distilled water and freeze at -80C or if not processed immediately.