RNA was extracted using TriZol standard protocol
Microarray results are analyzed by GeneSpring GX 11 software (Agilent Technologies).Data transformation is applied to set a threshold at 1.0 of raw signals, followed by on-chip quantile normalization and subsequent transformation to base 2 logarithm.
Images at 5 um resolution are generated by Agilent scanner and the Feature Extraction 10.5 software is used to obtain the microarray raw-data.
Hybridizations are performed at 55 degrees C for 17 hours in a rotating oven.
Labeled cRNA is synthesized from 500 ng of total RNA using the Low RNA Input Linear Amplification Kit (Agilent Technologies) in the presence of cyanine 3-CTP (Perkin-Elmer Life Sciences, Boston, MA).
RNA was extracted from A375 cells, treated for 12 days with 20 uM of efavirenz or DMSO