Total RNA was isolated from whole blood drawn into PAXgene tubes using the PAXgene Blood RNA kit (PreAnalytiX; Qiagen GmbH-USA). The quality and quantity of the RNA was confirmed using the Nanodrop 1000 Spectrophotomer (Thermo Fisher Scientific, Wilmington, DE) and by RT PCR.
Label
biotin
Label protocol
RNA was amplified and the cRNA was biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit (Life Technologies, Carlsbad, CA).
Hybridization protocol
Standard Illumina hybridization protocol
Scan protocol
Standard Illumina scanning protocol
Data processing
A comprehensive quality control process was performed on all arrays using the lumi package (version 2.6.0) in Bioconductor in the R environment (version 2.14.0) for statistical computing. Quality of the raw data was assessed using the percent of probes present, MA plots, boxplots of the expression distribution, and heatmaps to visualize the correlation between samples. Samples in which the percent of probes present was 15% or less were excluded. The lumi package was used to make background corrections, log-transform expression values, and carry out quantile normalization.
