Extended Data Figure 9: Validating the turnover process.

a, Six clonal populations from two WI38 passages were generated. b, The passage 23 clones are described earlier, and are consistent on average with the matching passage 23 non-clonal population. Passage 27 clones are sampled from a population of cells that are on average 16 cell cycles older than passage 23 cells. As shown in the density plot, this affects the average population in these cells as predicted by our model (decreased methylation at high methylation loci, some increased methylation in low methylation regions). c, Stratification of the turnover rates inferred independently from passage 27 clones given replication time, lamina binding and nucleosome occupancy. The trends are indistinguishable from those observed for passage 23 clones (Fig. 3). d, K562 methylation gain and loss rates stratified according to nucleosome occupancy (light blue, depleted; blue, occupied), time of replication (x-axis of each panel), and LaminB1 interaction (different panels organized from low (left) to high (right)). e, Design of a time series clonal expansion experiment that was based on sampling a clonal population at three time points, each time extracting approximately 500,000 cells for profiling and 400,000 for continuous expansion. f, Average turnover rates (estimated from pooled statistics of all consistently covered CpGs) in independent UMI-bis libraries from two clones and three time points. Each time point was analysed using the same approach with the only difference being the assumed depth of the exponential coalescent model (22, 27 and 30 cell divisions). We recovered remarkably consistent rates from each of the time points. Interestingly, we also observed global differences in the rates in WI9 and WI11 clones (for both gain and loss). One possible explanation for this may be the existence of a rapidly growing subpopulation (which is sampled at higher depth than expected by the symmetrical exponential growth model we assumed).