We measured the effect of docetaxel treatment to three differentially responsive prostate cancer cell lines, LNCaP, DU145 and PC-3, based on a transcriptional time course response by microarray analysis. These cell lines represent both androgen independent (DU145 and PC-3) and androgen sensitive (LNCaP) cells
Hybridized arrays were scanned with Agilent’s dual laser-based scanner. Feature Extraction software version 10.5 (Agilent Technologies) was used to link a feature to a design file and to determine the relative fluorescence intensity between two samples. Dye swap strategy with alternate cy3 and cy5 labeling on docetaxel treated and control groups over four time points was used to have technical replicates and decrease dye bias.