Fig. 2: Single-cell replication-state data, generated by multiple library preparation protocols.

a Single-cell replication profiles for 2242 GM12878 cells (including both sorted and unsorted cells), following single-cell isolation and library preparation with the 10x Genomics Single-Cell CNV Solution. Consistency of the replication program is observed across cells at chromosome scale and at the level of individual peaks (inset). Pileups reflect sharply defined and consistently replicated regions, which overlap peaks in the bulk replication-timing profile. Variation in activation time during S phase among initiation sites is also observed to mirror the replication-timing profile. Each row represents a single cell, sorted by the percent of the genome replicated, and each column represents a fixed-size window of 20 kb. In total, 195 cells are not shown due to copy-number aberrations on this chromosome. Low-mappability regions and cell-specific copy-number alterations have been masked (white). Insets show smaller regions. b Single-cell replication profiles for 519 GM18507 cells, following amplification-free direct DNA transposition single-cell library preparation (DLP+). Due to noise, only 480–614 of the 759 S-phase cells were analyzed for any given chromosome. Raw data are from¹⁸.