Identification of Suz12 target genes. (A) The number of genes commonly found on the two biological replicates of the Suz12 ChIP-chip experiments were compared in bins of 200, through the top 10,000 ranked genes on each list (Suz12). Also shown are the number of genes found to be in common using randomized Suz12 data sets (Random). Finally, the number of genes in common at each point in the comparison of the randomized data sets was subtracted from the number of genes in common in the two ranked Suz12 ChIP-chip data sets (Corrected). (B) PCR confirmations (using a third biological replicate of Suz12 amplicons) of Suz12 binding to a set of promoters identified in the ChIP-chip assays. All enrichments were normalized to the enrichment at the Wnt1 promoter. For these experiments, the number of PCR cycles was kept low to ensure that the signals were within the linear range of the assay, providing a semiquantitative analysis.
