normalization data transformation protocol
Signal intensities were background corrected and set at the minimum value of 128 if the intensity was below the minimum (this level is the average minimum intensity level detected in the experiments). Arrays were median centered using the median of all arrays. A probe was excluded if more than 50% of its data were missing or below the minimum intensity. All remaining probes for an miRNA were considered for differential expression.
array scanning protocol
Hybridization signals were detected by biotin binding of a Streptavidin-Alexa647 conjugate (one-color signal) using a GenePix 4000B scanner (Axon Instruments). We quantified images using the GenePix Pro 6.0 (Axon Instruments).
nucleic acid hybridization to array protocol
Hybridization was carried out on version 5 of the MDACC miRNA expression bioarray.
nucleic acid labeling protocol
Five ug of total RNA from each sample was labeled with biotin by reverse transcription using random octomers.
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).