6 protocols
nucleic_acid extraction
RNA was extracted using TriZol standard protocol
normalization data transformation 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
array scanning and feature extraction protocol
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
nucleic acid hybridization to array protocol
Hybridizations are performed at 55 degrees C for 17 hours in a rotating oven
nucleic acid labeling protocol
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)
treatment protocol
RNA was extracted from A375 cells, treated for 12 days with 20 uM of efavirenz or DMSO