RNA was amplified using the Sigma whole transcriptome amplification kits following the manufacturer’s protocol (Sigma-Aldrich, St Louis, MO), and subsequent Cy3-CTP labeling was performed using NimbleGen one-color labeling kits (Roche-NimbleGen Inc, Madison, WI). Labeled Cy3-cDNA was assessed using the Nandrop ND-8000 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome.
Hybridization protocol
Hybridizations were performed for 17 hrs, according to the manufacturers protocol.
Scan protocol
Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.
Data processing
This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
