Agilent Bioanalyzer (Agilent Technologies USA). Starting with 200 ng of RNA, the Ambion Illumina TotalPrep Amplification Kit was used for anti-sense RNA synthesis, amplification, and purification according to the protocol provided by the manufacturer (Ambion, USA). 750 ng of complementary RNA was hybridized to Illumina HumanHT12 BeadChips and scanned on the Illumina BeadArray Reader. Expression data preprocessing was as mentioned before. We first attempted to replicate the trait-associated trans-eQTLs per tissue, using an FDR of 0.05 and 100 permutations. Subsequently we conducted a meta-analysis, combining the four tissues. Per trans-eQTL we used a weighted Z-method to combine the four individual p-values. However, these four datasets are not independent, as they reflect the same individuals. We resolved this by conducting the permutations in such a way that in every permutation round the samples were permuted in exactly the same way for each of the four tissues. By doing this we retained the correlations that exist between the different tissues per sample, and were able to get a realistic empiric (null-)distribution of expected test-statistics.
