Total RNA from naïve and, where available, treated monocytes from each individual was quantified using the Illumina HumanHT-12 v4 BeadChip gene expression array platform with 47,231 probes. Of these, 28,688 probes correspond to coding transcripts with well-established annotations (RefSeq content NM), 11,121 to coding transcript with provisional annotation (XM), 1752 to noncoding transcript with well-established annotation (NR), 2209 to noncoding transcript with provisional annotation (XR), and 3461 to experimentally confirmed mRNA sequences that align to expressed sequence tag (EST) clusters from UniGene. Analysis of 1488 arrays was performed in three separate batches, the first consisting of 288 naïve monocyte samples as previously described (8). The second batch consisted of 636 samples from the same individuals randomized to individual and treatment across array. A third batch consisted of 564 samples composed of 144 further naïve monocyte samples, as well as 420 treated samples that were similarly randomized to individual and treatment across arrays. Complementary RNA synthesis, cleanup, and hybridization were as per the manufacturer’s instructions. Arrays were read, and data were exported using BeadStudio software (Illumina). Samples were subsequently processed in
