Figure 3

MLPA on DNA from HeLa cells. A) Representative MLPA peak patterns obtained from nuclei isolated from HeLa cells and subsequent treatment with 0, 0.5 and 2 units of DNaseI. Red peaks represent size standards, blue peaks the signals from the probes after PCR amplification. Black numbers show probes designed to bind to non-sensitive regions, blue numbers to sensitive regions for HeLa cells as published by the ENCODE consortium. B) Analysis of experiment shown in 3A. Data were obtained from two independent experiments and two technical replicates (n = 4). Results shown as mean ± SD. C) Analysis of data derived from DNaseI treatment of naked DNA isolated from HeLa cells. In this case DNaseI digestion was with either 0.25 units or 1 unit DNaseI for 1 minute on ice, as this DNA was far more susceptible to degradation than DNA in intact nuclei. Probes are grouped into sensitive and non-sensitive, and then ordered according to their length. N: non-sensitive, S: sensitive for HeLa cells as published by the ENCODE consortium.