Ten nanograms of total RNA were amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA).
Hybridization protocol
The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)
Scan protocol
standard Affymetrix protocol
Data processing
Transcript levels were processed from data image files using RMA method, implemented by Bioconductor R package. To reduce batch effects, transcript levels were further corrected with the ComBat method (Johnson, 2007), which applies empirical Bayes framework for adjusting data for batch effects. Final dataset which was used in the paper and contains 8968 genes is included in the supplementary file GSE24759_data.sort.txt.
