Extended Data Fig. 1: Genomic stability and cell cycle determination in the PF1 line.

a, Divisions per day on the Phenomex instrument and in cell culture. Rates for cells split after a single mitosis are noted. Numbers above boxes represent the total number of rates measured, for Phenomex this reflects pens, for incubator cells it is individual wells. Red numbers represent the mean doubling time in hours. Boxplot elements are as described in Fig. 3c, albeit without notches. Proliferation measurements from the Phenomex platform were taken on cells that proliferated post UV treatment. b, Copy Number analysis, showing diploid content for most of the genome. Reads were counted in 10 kb bins, and the y axis represents log2(distance to mean across all bins). Red vertical lines demarcate chromosome boundaries, and green horizontal lines represent counts expected for a single copy number gain or loss. c, Top: DNA content (x axis = Hoechst intensity) as a function of green and red fluorescence. Histogram bins have been colored by scaled log2(red/green) for each cell. Bottom: FUCCI fluorophores imaging over time. 357 cells on one chip were affinity propagation clustered based on FUCCI across all 6 timepoints. Color scale is noted above and is identical to the Hoechst histogram color scheme. Doubling time point (DT) is indicated by the second annotation column scaling from early replicating timepoints (gray) to later replication timepoints (dark blue). Timepoints are 3 hour intervals and noted below each column. d, Fluorophore signal per cell cycle and theoretical effect of ploidy on mutation patterns for pulse mutagenesis (UV). Cells in S-phase would have intermittent lesion segregation patterns, while cells with duplicated DNA (G2/M) would not show lesion segregation patterns after a single mitosis. e, Scatter of scaled G1 (red) and G2/M (green) signal directly after penning for 1120 cells measured on the Phenomex platform. Cells to split are indicated by the white dashed box. f, Gating Live cells with FSC-area by SSC-area. g, Singlet determination by FSC-area by FSC-height. h, Fluorophore intensity for G1 fluorophore (FITC) and G2/M fluorophore (yellow-green laser) as measured by FACs. White box denotes FITC positive cells that were single-cell sorted to establish the PF1 line.