Increase in anti-5-methyl-C antibody concentration increases the efficiency of IP. qPCR was used to quantitate various regions of the fully methylated target DNA to determine the percentage of pull down, calculated by dividing the amount of DNA after IP by the amount of input DNA, with different concentrations of the antibody for the IP. A) A schematic diagram of MseI restriction sites on pCLH22. MseI restriction sites are as marked by short lines on the circle and the nucleotide positions of DNA fragments examined are as numbered. The solid arrows indicate the locations of the qPCR amplicons with the number of CpG sites in the box under the name of each probe/primer set. The hollow arrows mark the regions examined by sodium bisulfite sequencing. B) Percentage of IP using different concentrations of antibody and no antibody with fully methylated pCLH22 as target. C) Percentage of IP using different concentrations of antibody and no antibody with entirely unmethylated pCLH22 as target.