We followed the scRepli-seq protocol as described (Miura et al., 2020). Early-S phase cell population were sorted by a Sony SH800 cell sorter (thymidine/5-Ph-IAA removed cells: ultra-purity mode, G1/early-S cells: single-cell mode). Thymidine/5-Ph-IAA removed cells were manually collected after EdU signal observation and cells were transferred into lysis buffer using mouth pipette. G1/early-S cells were directly sorted into lysis buffer. Extracted gDNA samples were subject to whole-genome amplification (WGA) with a SeqPlex kit (Sigma, SEQXE). NGS libraries were constructed WGA DNA with an NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer's instructions.