6 protocols
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
hybridization protocol
Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60 Agilent® Microarray chip (ID: G4858A-028004) using Gene Expression Hybridization Kit Cat. # 5188-5242).
labelling protocol
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).
growth protocol
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).