Figure 4. ChIP-on-chip map of changes in RNA-Polymerase-II (Pol-II) association around transcription start sites on chromosome 6 in P2 and P25 mouse neural retina. ChIP was performed using an antibody specific for RNA polymerase-II. ChIP DNA was amplified, labeled, and hybridized onto Affymetrix gene chip mouse promoter tiling arrays (v.1), as detailed in the methods. Probe intensity data were normalized to total genomic DNA (non-ChIP) and the linear scaling format option. Chromosome 6 data are shown here for age P2 (Pol-II P2) and age P25 (Pol-II P25), including a plot of the Pol-II signal ratio (P25/P2 ratio). The horizontal line indicates the Pol-II peak signal ratio (1.8) selected to predict an increased activation state during terminal maturation of photoreceptors. This value was validated through follow-up analysis of the test gene set representing a full range of Pol-II peak signal ratios (Table 1). The locations of many genes displaying activation increases are readily visible. Some examples include Rhodopsin (Rho), Transducin-γ subunit (Gngt1), Aquaporin (Aqp1), and Na: neurotransporter symporter for taurine and β-alanine (Slc6a6).