Total RNA were extracted from frozen tumor samples using the miRNeasy® Mini Kit (Qiagen) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Label
Cy3
Label protocol
RNA was labeled according to manufacturer’s protocol.
Hybridization protocol
Gene expression analysis was carried out using Agilent Whole human 44K Genome Oligo Array (G4112F; Agilent Technologies, Santa Clara, CA, USA), according to the manufacturer’s protocol.
Scan protocol
the scan was performed according to manufacturer’s recommendations with scanning resolution of 5µm
Data processing
For each series all microarrays were simultaneously normalized using the Quantile algorithm.
