In brief

Usually, the protocol developed to analyze genome-wide replication-timing program in mammalian cells lasts 3 weeks (Ryba et al., 2011). The BrdU immunoprecipitation is a time consuming step and need to be carefully monitored in order to get most precise and specific signals. Here, we modified the previous protocol by introducing an automated step using the SX-8G IP-Star® Compact Automated System to perform the BrdU immunoprecipitation step (DNA-IP). This accelerated the protocol and improved the reproducibility of the DNA-IP experiment. Indeed, the automated system allows performing DNA-IP overnight and reduces the signal-to-noise ratio. It also provides high standardization of the DNA-IP step, allowing strong reproducibility of RT profiles from one experiment to another.