Total RNA was extracted from frozen (–80°C) tumor samples using a standard Trizol procedure. Frozen samples were shattered in liquid nitrogen and homogenized in 1 ml TRIzol (Invitrogen, Carlsbad, USA). Extraction was performed using a standard chloroform/isopropanol method. RNA pellets were resuspended in RNase-free water, subjected to a Qiagen clean up step and stored at -80°C.
Label
biotin
Label protocol
According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).
Hybridization protocol
According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).
Scan protocol
According to the manufacturer's protocol (Affymetrix, Santa Clara, CA).
Description
MERLION_X00K01639
Data processing
The expression microarray data were standardized and normalized using the robust multi-array average (RMA) procedure [22]. Genes whose maximum expression did not exceed the median value of expression or whose interquartile range (IQR) did not exceed the first quartile of the IQR distribution were excluded. A total of 37,771 probe sets were considered for analysis.
