Total cellular RNA was purified using Trizol reagent, quantified using UV spectroscopy (Nanodrop Technologies, Wilmington,DE) and qualitatively assessed using an Experian Bioanalyzer (Hercules,CA). Amplified cDNA was prepared from 20ng of total RNA using the whole transcript WT-Ovation TM RNA Amplification System.
Label
biotin
Label protocol
Amplified cDNA was biotin labeled using the Encore Biotin Module (NuGen Technologies, San Carlos, CA) according to the manufacturer’s instructions.
Hybridization protocol
Labeled targets were then hybridized to Mouse Exon 1.0S T arrays (Affymetrix, Santa Clara, CA).
Scan protocol
GeneChips were scanned using Affymetrix GeneArray scanner GS 3000.
Data processing
Raw data were processed with the RMA algorithm in Affymetrix Expression ConsoleTM version1.1 (Affymetrix Inc., USA).
This analysis included core exons. Probe-group file: MoEx-1_0-st-v1.r2.pgf Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps
