Embryonic development proceeds as a series of orderly cell state transitions built upon noisy molecular processes. Here, we defined gene expression and cell motion states using single cell RNA sequencing data and in vivo timelapse cell tracking data of the zebrafish tailbud. We performed a parallel identification of these states using dimensional reduction methods and a change point detection algorithm. Both types of cell states were quantitatively mapped onto embryos, and we utilized the cell motion states to study the dynamics of biological state transitions over time. The time average pattern of cell motion states is reproducible among embryos. However, individual embryos exhibit transient deviations from the time average forming left-right asymmetries in collective cell motion. Thus, the reproducible pattern of cell states and bilateral symmetry arises from temporal averaging. In addition, collective cell behavior can be a source of asymmetry rather than a buffer against noisy individual cell behavior.

Zebrafish embryos were injected the mRNA encoding H2A-mRFP at the one-cell stage and then incubated until the 8-somite stage. They were mounted dorsal side up and the tailbud was imaged on a point-scanning confocal every three minutes for up to three hours. Cells were tracked using Imaris. Data was collected on wild-type embryos and those subject to signalling perturbations. Specifically, starting at the 6-somite stage embryos were incubated in 50 mM of SU5402 or 40 mM of DMH1 for two hours to inhibit FGF or BMP signaling, respectively. Wnt signaling was inhibited by injecting notum-1 mRNA at a concentration of 150 ng/mL into embryos at the single cell stage and then incubating them until the 10-somite stage. This treatment yields a phenotypic spectrum, and embryos with nascent body elongation defects were chosen for further experiments.