Custom 44 K tiling arrays were designed using eArray (Agilent technologies). Probes of approximately 55 bp were selected to tile all unique regions within approximately 3.5 MB upstream and downstream of the NR3C1 gene described in Ensembl (version 44) at 100 bp-spacing. Probe intensities were extracted from hybridization images using Agilent's Feature Extraction 9.5.3 Image Analysis Software and analyzed using the R software environment for statistical computing[51]. Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray. Each microarray was normalized using quantile-normalization[52] assuming an identical overall distribution of measurement across all samples. Gene expression levels were estimated as the mean probe values across exons. DNA methylation and H3K9 acetylation levels at genomic locations were estimated using a Bayesian convolution algorithm to incorporate probe values from nearby probes[53]. Gene expression differences associated with maternal care were obtained using RMA[54] applied to sample probe values inside exons. RDme/ac were identified by computing a modified t-statistic for each probe and then significant levels of agreement across 1000 bp regions. Enrichment of RDac and RDme was determined
