Rapid high-resolution measurement of DNA replication timing by droplet digital PCR

Time of DNA replication is inversely proportional to the relative DNA copy number. Sort-seq is a technique that uses deep short read sequencing to determine relative copy number across genome from sorted S phase cells. We have applied sort-seq to HeLa cells and report their relative copy number profile. The high (close to 2) value means the region replicates early in S phase; the low (close to 1) value means the region is replicated late in S phase. Proliferating HeLa cells were sorted to enrich for G1 and S phase cell cycle stages (based on propidium iodide staining). Extracted DNA was fragmented and sequenced on Illumina NextSeq platform.