Cells were grown to a density of 1.5E6 cells/ml and treated with 1mM hydroxyurea for 3 hours to stall replication forks and activate the intra-S-phase checkpoint. BrdU was added at 50ug/ml and cells were incubated for another 20 hours, resulting in labeling only of DNA sequences immediately adjacent to early activating origins of replication. Cells were frozen.
Quantile normalization was applied across arrays. Peaks were called with a p-value threshold of 0.001 using MA2C. The union of early activating origins of replication from all 3 cell lines was taken to generate a set of meta-peaks; each meta-peak represents a contiguous region covered by an early activating origin of replication present in at least one cell line. In total, 823 meta-peaks were called, 195 common to all three cell lines.