RNA isolation from liver tissues was performed using Trizol (Invitrogen, Paisley, UK) extraction and Qiagen RNeasy-mini kit (Qiagen, Valencia, CA, USA) with on-column DNase treatment as described previously.23 Only high-quality RNA preparations according to Agilent Bioanalyzer (Nano-Lab Chip Kit, Agilent Technologies, Waldbronn, Germany) RNA Integrity Number (RIN) assignment (>7) were used in this study. In all, 200 ng of total RNA was amplified and labeled using the Illumina TotalPrep RNA amplification kit (Ambion Applied Biosystems, Darmstadt, Germany). cRNA quality was assessed by capillary electrophoresis on Agilent 2 100 Bioanalyzer (Agilent Technologies). Expression levels of >48 000 mRNA transcripts were assessed by Human-WG6v2 Expression BeadChip (Illumina, Eindhoven, The Netherlands). Hybridization was carried out according to the manufacturer's instructions. Genome-wide SNP data had been generated from genomic DNA using the HumanHap300 Genotyping BeadChip (Illumina) with 318 237 SNPs as described before.24 A comparison with the microarray platforms used in the Seattle study is shown in Figure 1. All data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE32504 (http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE32504).
