title: Repli-seq of early S phase fraction: Rif1 knockout mESC
design: Genome-wide RT profiles were constructed as previously described.  Briefly, cells were pulse labeled with BrdU for 2 hours and separated into  early and late S-phase fractions by Propidium iodide staining and flow  cytometry. BrdU-substituted DNA from 40k early and late S-phase cells was  immunoprecipitated by anti-BrdU antibody (Becton Dickinson 347580)Sequencing  libraries were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina  (E7370).