Validation of DNase clusters by real-time PCR. Delta (Δ) Ct values represent the number of additional cycles to achieve threshold amplification from nuclear DNA treated with DNase I compared with nuclear DNA not treated with DNase I. (A) Most primer sets that flank random regions of the genome display Δ Ct values less than two. Approximately 20% of primer sets that flank sequences from the DNase library that do not cluster with other sequences display Δ Ct values greater than two. Eighty percent of primer sets that flank DNase clusters of two or more display Δ Ct values greater than two. (B) The percentage of primer sets that have Δ Ct values greater than two was determined for each cluster size (% validated sites). Clusters of two were ∼50% accurate at identifying valid HS sites, while clusters of three or more were highly accurate at identifying valid HS sites. (C) The distribution of Δ Ct values was determined for different cluster sizes. Note that the highest cluster sizes have the highest Δ Ct values.
