normalization data transformation protocol
The data were normalized with Bioconductor software using quantiles. ID_REF = VALUE = Quantile-normalized log2 signal intensity
array scanning protocol
Microarray Scanner Agilent G2505X class C
Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60 Agilent® Microarray chip (ID: G4858A-028004) using Gene Expression Hybridization Kit Cat. # 5188-5242).
For future sample normalization, RNA was treated with One-Color RNA Spike-In Kit cat. # 5188-5282 (Agilent). 200ng of RNA were used for cDNA preparation with Low Input Quick Amp Labeling Kit, one-color Cat. # 5190-2305, Agilent®. Sample labelling with dye (Cy3) fluorophore was made with previous cited kit. Labelled cDNA was purified with RNeasy MinElute Cleanup Kit Cat.# 74204 (Izasa/Qiagen).
Surgical resection of normal colorectal tissue samples.
nucleic acid extraction protocol
The samples were homogenized with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).