normalization data transformation protocol
The raw data were processed by the Robust Multi-array Average (RMA) algorithm implemented in the affy package in R using default settings.
array scanning protocol
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
nucleic acid hybridization to array protocol
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
nucleic acid labeling protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Cells were grown on culture plates at 37C with 5% carbon dioxide. LUC and LUL2 cells were grown in MEM (Gibco) + 10% FBS. T24 and FL4 cells were grown in DMEM/F12 (Gibco) + 5% FBS.
nucleic acid extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Cells growing on culture plates were rinsed with ice-cold PBS and lysed on ice in the Trizol solution (Invitrogen).