Fig. 6

Agent-based modelling results for Nanog-dependent or Mycn-dependent cell-cycle (a, b) Nanog-dependent cell-cycle model simulations. a The blue line depicts the Nanog-dependent cell-cycle model fitted to serum/LIF proliferation data (data shown as solid black line, RMSE 2.35), while the red line is the predicted cell-growth in 2i/LIF (RMSE 22.59 as compared to 2i/LIF data, shown as dashed black line). Each cell cycle was independently sampled from a normal distribution with mean 8.5 h for NH and 13.5 h for NL, and standard deviation 1 h for both NH and NL. b The red line shows fitting of the Nanog-dependent cell-cycle model to 2i/LIF data (RMSE 1.07), with prediction of growth in serum/LIF plotted in blue (RMSE 11.01); cell cycles were allocated with mean 13.175 h for NH and 20.925 h for NL. c, d Mycn-dependent cell-cycle model simulations. c The blue line depicts the Mycn-dependent cell-cycle model fitted to serum/LIF data (solid black line, RMSE 2.02), while the red line is the predicted cell growth in 2i/LIF (data shown as dashed black line, RMSE 3.08). In this case the cell cycles were allocated from a normal distribution with mean 8.5 h for Mycn High (MH) and 15 h for Mycn Low (ML). d The red line shows the Mycn-dependent cell-cycle model fitted to 2i/LIF data (RMSE 1.33) with serum/LIF predicted growth dynamics plotted in blue (RMSE 4.41). The cell cycles were allocated with means 9.5 h for MH and 16 h for ML. (e) Agent-based simulations of Nanog sorting experiment (Mycn-dependent cell-cycle model) in serum/LIF. The red and blue lines depict the changing ratio of NH cells in the population starting from NH or NL state, respectively. In a–d, data are the average of four independent experiments. Cell count, performed every 24 h for 3 days, is plotted as fold change vs. count at day 0; Standard Error (SE) is shown as a shaded grey region. In a–e, all model simulations are the average of 15 independent simulations, with the shaded regions showing SE