normalization data transformation protocol
The data were analyzed using R 3.0.1, affy package version 1.34.0 & 1.38.1, farms package version 1.12.0 and Entrez based alternative CDF version 15.1.0 for probeset annotation ID_REF = VALUE = I/NI filtered FARMS (lfarms) summarized values
array scanning protocol
Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).
Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).
All microarray related steps for target preparation including amplification of total RNA and labeling were carried out as described in the GeneChip®3’ IVT, Express Kit User Manual , (Affymetrix 2004).
sample treatment protocol
LNCaP cells were incubated with compound 8 h. DMSO was used as negative control.
nucleic acid extraction protocol
Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).
Human prostate (LnCaP cells, ATCC CRL-1740) were cultured using modified ATCC-formulated RPMI-1640 Medium, Catalog No. 30-2001 (Composition: 500 ml RPMI 1640 , 5.7 ml L-glutamine 2mM, 57 ml FBS (not heat inactivated), 5.7 ml Gentamycine (50 µg/ml)), complemented with fetal bovine serum to a final concentration of 10% and with 1% of L-glutamine and Gentamycine. Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.