Optimizing scheduling in dual-pulse nucleoside labeling experiments for cell cycle analysis

All eukaryotic cells go though a universal sequence of phases during their division cycle, where the phase timings vary according to cell type and state. Dual-pulse nucleoside labeling (DPNL) is a standard, widely applicable experimental DNA base substituting technique to probe cell cycle kinetics at the population level, including in living organisms. In such an experimental protocol, a key scheduling parameter is the choice of waiting time between the two labeling pulses. Here, we model population cell cycle dynamics as a three-stage Poisson process with an idealized S-phase labeling step, and use a simulation-based look-up procedure to demonstrate that the inter-pulse waiting time can be optimized to maximize the signal-to-noise ratio of inferred cycle parameters - an issue that is especially critical in DPNL experiments with limited cell numbers and replicates. An optimal choice of pulse scheduling typically improves S phase time inference by 50% compared to a random choice. We further discuss the procedure to perform such a task in an experimentally relevant setting.