Beadarray reader software

Total RNA was extracted using RNeasy Mini Kit (Qiagen). 500 ng total RNA was used for cRNA amplification using Illumina TotalPrep RNA Amplification kit (Ambion), following manufacturers’ instructions. 750 ng cRNA was then hybridized onto the HumanRef-8 v2 Sentrix BeadChip (Illumina). Subsequently, the fluorescence emission by Cy3 was quantitatively detected by the Illumina BeadArray Reader software for downstream analysis of data by Partek software. Statistical significance of individual gene expression levels was analyzed by Analysis of variance (ANOVA) and significant genes were identified based on fold-changes. Threshold for significance was set at fold-change > ± |2.0| when compared to control cells. Absolute intensity differences between experimental groups were set at p < 0.05. All data is MIAME compliant and the raw data has been deposited in a MIAME compliant database (accession number: GSE24097).

This analysis was performed by the Norwegian Genomics Consortium (Oslo, Norway). Briefly, cRNA synthesis, amplification, and hybridization to Illumina Human WG-6 v3 Expression BeadChip arrays (Illumina, Inc., San Diego, CA, USA), containing 48,000 probes, were carried out as per manufacturer's instructions. Signal intensities were extracted by the BeadArray Reader Software (Illumina), and raw data were imported into the GenomeStudio v2010.1 Software, Gene Expression module v1.6.0 (Illumina). The primary array data are available in the Gene Expression Omnibus data repository (GEO accession number GSE46703).