Single-cell DNA replication sequencing (scRepli-seq): a method for mapping replication timing domains genome wide in single mammalian cells

Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require a large number of S-phase cells for either effective enrichment of replicating DNA through BrdU immunoprecipitation or the determination of copy number differences during S-phase, which restricts their application to non-abundant cell types. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on the whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy number differences that arise between replicated and unreplicated DNA. We also provide computational pipelines that are key components of the methodology. NGS library preparation takes 3 d. Overall design: Single-cell Repli-seq experiments in hTERT-RPE1. We deposited single-cell data sets passed (or not passed) by our MAD score-based quality control. Total 26 samples.