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Chunk #54 — Materials and Methods — Microarray Design, Hybridization, Scanning and Analysis

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Differential DNA methylation regions in cytokine and transcription factor genomic loci associate with childhood physical aggression.
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The identification of regulatory elements contained in the cytokine and TF loci shown in the figures and tables were obtained using the Encyclopedia of DNA Elements (ENCODE) tracks from the UCSC genome browser (http://genome.ucsc.edu/ENCODE/). The transcription factors binding sites and DNase hypersensitive sites (cluster) shown were obtained from ChIP-seq data done on 24 different cell lines. The histone marks shown were also obtained from ChIP-seq data done on 8 different cell lines but we selected only two cell lines relevant to the lymphocytes analyzed in our study, Gm12878 and K562.