Cdx2-eGFP embryos were always staged based on cell number, which we determined in live embryos based on the number of Cdx2-eGFP positive cells present. An additional layer of ‘early’ and ‘late’ sub-staging was included, which refers to the time of embryo isolation. For example ‘early 16 cell’ embryos were harvested at E2.5 – a time point when the population of embryos are between 8 and 16 cell stages – but only 16 cell embryos were used (embryos with average of 12 visible Cdx2-eGFP positive cells). Or ‘late 16 cell’ embryos were harvested at E2.75 -when embryos are between 16- and 32 cells - however only strictly 16 cell embryos (embryos with average of 12 visible Cdx2-eGFP positive cells) were used from this time point. We established criteria for staging using the number of Cdx2-eGFP positive cells in live embryos. Graph above shows average number of Cdx2-eGFP positive cells in live staged embryos at each stage (8 cell n = 10, early 16 cell n = 14, late 16 cell n = 19, early 32 cell n = 21, late 32 cell n = 24, ~64 cell n = 11 and ~80 cell n = 14). A subset of staged embryos were fixed and total cell numbers were determined by Dapi staining (8 cell n = 10, early 16 cell n = 14, late 16 cell n = 15, early 32 cell n = 21, late 32 cell n = 24, ~64 cell n = 11 and ~80 cell n = 11). Error bars indicate standard deviation of mean. Using this guide, only carefully staged embryos were used at each time point for all experiments in the study.