Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Label
biotin
Label protocol
400 ng of total RNA were used to perform target preparation using Message Amp II-biotin Enhanced reagents (Life Technologies).
Hybridization protocol
Arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at 45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).
Scan protocol
Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)
Description
Pool of 50 resected ventrical samples, 2 weeks after surgery
Data processing
Background subtraction and quantile normalization were performed using the R/Bioconductor package affy, rma method
