Embryos were collected and precisely staged based on morphological features, including by counting somite numbers (up to E10) and an automated process that leverages limb bud geometry (E10E15) (Methods). Each embryo was assigned to one of 45 temporal bins at 6-h increments from E8 to P0, and to more highly resolved 2-h bins at earlier timepoints based on somite counts (034 somites). The first three bins (E8.0, E8.25 and E8.5) are combined. Embryos with somite counts 1, 13 and 19 are missing from the series (blue ticks in sub-axis). The number (log 2 scale) of nuclei profiled at each timepoint, is shown adjacent to the horizontal timeline, for 2-h bins (034 somites) for E8E10 and for 6-h bins for E8P0.
