10 ug total RNA was amplified and labelled using Ambion Amino Allyl MessageAmp II aRNA Amplification Kit per the manufacturer's protocol.
Raw array data were read into J-Express Pro and filtered for controlls and saturated, non-uniform, population outliers, or low intensity spots. The data were stored as log2(experiment/control).
Scanning was performed with an Agilent G2505B DNA Microarray scanner using default parameters (100% PMT, 10 um resolution) at RT. Microarray images were analysed using Agilent Feature Extraction software version 126.96.36.199
Labelled cRNA corresponding to 20 pmol cyanine dye each of experimental and UHR samples were mixed and hybridized to Agilent Whole Human Genome Oligo Microarrays (1x44k format) per manufacturer's 60-mer oligo microarray processing protocol (Ver. 4.1)
Tissue samples were obtained as core needle biopsies using a 16 Gauge core needle under ultrasound guidance and immediately placed into RNAlater. The stabilized samples were stored at -80 C until processing.
RNA was isolated with Trizol per the manufacturer's protocol.