Hybridization of Cot-enriched mononucleosomal DNA fragments to a tiling microarray. Gel-purified Cot-enriched mononucleosomal DNA was labeled with Cy3, and sonicated Cot-enriched bare genomic DNA was labeled with Cy5; both were hybridized to a tiling microarray containing (A,B) the MMTV LTR and (C,D) the promoter region of the LCMT2 gene. Probes were 50 bases long and spaced 20 bases apart. Each probe was spotted in triplicate on both the forward and reverse strands. Replicate probe data from MMTV (A) and LCMT2 (C) are shown as the log2 ratio of mononucleosomal DNA (Cy3) to bare genomic DNA (Cy5). (B,D) Each probe from the six replicate data sets (three from the forward strand and three from the reverse strand) was log-transformed, normalized, and plotted as log ratios for MMTV (B) and LCMT2 (D).
