Normalization and correction for batch and incubator effects were carried out on all probes. Probes were subsequently selected for eQTL analysis. As previously described (8), probe sequences mapping to more than one genomic location using Basic Local Alignment Search Tool (BLAST) were excluded from eQTL analysis. Additionally, 6137 probes found to anneal in regions with SNPs present at a MAF of at least 1% in the European population of the 1000 Genomes Project were excluded from eQTL analysis to minimize potential confounding effects, as were probes mapping to non-autosomal locations. Remaining probes were included in eQTL analysis if they were present (Illumina detection P < 0.01) in >2.5% of samples from a specific treatment or, alternatively, >5% of all samples. This resulted in 15,421 probes for analysis, mapping to 11,168 independent Entrez ID.
