(A) Mating scheme for generating SOX2-SE-TG and MIR290-SE-TG mice and heterozygous pre-implantation embryos genetically carry 129SE-RGM-tdTomato and CASTSE-RGM-eGFP at the Sox2 or the Mir290 SE for imaging analyses. (B) live 4–8 cell (MIR290-SE-TG) and morula stage (SOX2-SE-TG) embryos. (C) Live E3.5-E4.5 blastocysts of SOX2-SE-TG and MIR290-SE-TG in 10x low magnification, 40x high magnification, and 3D projections (left to right in each group). Red: tdTomato, green: eGFP, blue: Hoechst 33342. (D) Tracking Sox2 SE DNA methylation dynamics in vivo. Columns are sorted and injected populations and rows are different imaging channels. Red: RGM-tdTomato; Green: RGM-eGFP; Cy5: Qtracker™ 705 was used to label and track injected cells. White arrows indicate demethylation, and yellow arrows de novo methylation, at 2 days post-injection compare to 5hr post-injection. Channels were adjusted for brightness and contrast for optimal visibility. See also Figure S7.