Human wg 6 v3 beadchips

RNA was extracted from cells using the Trizol method. RNA samples were cleaned up using RNEasy plus micro kit and run on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to ensure RNA integrity for whole genome studies. cRNA was prepared, hybridized to Cy3, loaded as singlicates on to Human WG-6 v3 beadchips (Illumina, Inc, San Diego, CA, USA), and scanned using an Illumina iScan reader. All data were quantile normalized, exported into text files using Bead studio software and data analyses were performed using box plots in JMP genomics (Version 3.0, SAS Institute Inc., Cary, NC, USA). Student’s T test was used in JMP to analyze values, with a Benjamini Hochberg False Discovery Rate (FDR) correction of 1%, alpha=0.05, and a cutoff of −log₁₀ (p value)>1.5. The list of significant genes obtained was imported into Ingenuity pathway analyses (IPA, Ingenuity® Systems, Redwood City, CA, USA) for identification of altered pathways/disease.