Fig. 6. ChIP/qPCR validation of Pol II-positive and -negative promoters. (A) Randomly selected Pol II-positive and -negative promoters scored by ChIP-DSL in Fig.1B. The y axis represents the ratio of array intensities. The promoters are arranged from high to low enrichment, with Pol II-positive promoters indicated by black bars and negative promoters by gray bars. (B) Validation by ChIP/qPCR analysis. Two control genomic regions (two gray bars at the end) were used to provide a base line to score Pol II-positive and -negative promoters. The y axis represents the percentage of signal over a fixed amount of input DNA. The data are summarized in Fig. 2B.

Fig. 7. ChIP-DSL analysis of MCF-7 cells using a control IgG and anti-ERa. ChIP-DSL reactions were carried out with E₂-stimulated MCF-7 cells using a control IgG (Left), vehicle-treated MCF-7 cells using anti-ERa (Center), and E₂-stimulated MCF-7 cells using anti-ERa (Right). PCR-amplified products were hybridized to an array containing »2,000 human promoters in these studies. Approximately 90% of ERa-positive signals in vehicle-treated cells were also scored positive in E₂-treated MCF-7 cells, including well known ERa target promoters.