i. Normalizeeach ChIP DNA fractions’ Ct value to the Input DNA fraction Ct value for the same qPCR Assay (ΔCt) to account forchromatin sample preparation differences. ΔCt [normalized ChIP] = (Ct [ChIP] - (Ct [Input] -Log2 (Input Dilution Factor))) Where, Input Dilution Factor = (fraction of theinput chromatin saved)-1 Average normalized ChIP Ct values for replicate samples. ii. Calculate the % Input for each ChIP fraction(linear conversion of the normalized ChIP ΔCt). % Input = 2 (-ΔCt [normalized ChIP]) iii. Adjust the normalized ChIP fraction Ct valuefor the normalized background (NIS/mock IP) fraction Ct value (first ΔΔCt). ΔΔCt [ChIP/NIS] = ΔCt [normalized ChIP] - ΔCt[normalized NIS/mock] iv. Calculate Assay Site IP Fold Enrichment abovethe sample specific background (linear conversion of the first ΔΔCt). Fold Enrichment = 2 (-ΔΔCt [ChIP/NIS]) v. Determine the difference between the normalizedexperimental sample (S2) and the control sample (S1) ChIP fraction Ct values(second ΔΔCt). ΔΔCt [S2-S1] = ΔCt [S2:normalized ChIP] - ΔCt[S1:normalized ChIP] vi. Calculate Differential Occupancy Fold Change(linear conversion of the second ΔΔCt to yield a fold change in site occupancy). Fold Change in Occupancy = 2 (-ΔΔCt [S2-S1])