array scanning protocol
Arrays were scanned using an Illumina Bead array Reader (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) following the manufacturer's procedure.
normalization data transformation protocol
Data processing of arrays were performed using Illumina BeadStudio software. Gene expression data was normalized using Quantile normalization and log2 transformation. Sample Gene Profile option of Illumina BeadStudio was used to export to a data matrix. ID_REF = VALUE = Log2 transformed normalized signal intensity.
Labeled cRNA (750 ng per array) was hybridized to the Illumina HumanHT-12 v4 expression beadchip according to the manufacturer's procedure (Illumina, Inc., San Diego, CA).
Biotin-labeled cRNA samples were prepared for hybridization using TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX) following the sample labeling procedure: Total RNA (500 ng) was used for cDNA synthesis. Amplification/labeling step (in vitro transcription) was then performed to synthesize biotin-labeled cRNA. Concentration of cRNA was then measured by spectrophotometer (Nanodrop, ND-1000)
nucleic acid extraction protocol
Total RNA was extracted from cells using the PureLink™ RNA Mini kit (Ambion) following the manufacturer protocol.