Mouse embryonic stem cell lines for imaging the Pou5f1 and Nanog loci were derived from Bruce 4 mESCs (Millipore Sigma CMTI-2; murine strain C57/BL6J, male – species/sex verified by karyotyping, no additional cell line authentification performed). OMG mESCs39 (link) contain a 24 × MS2 cassette integrated in the 3′-UTR of one of the two Pou5f1 alleles57 (link) and also stably express MCP-mNeonGreen39 (link). NMG mESCs contain 24 × MS2 cassettes integrated in the 3′-UTR of both Nanog alleles and also stably express MCP-mNeonGreen58 (link). NMG SNAP-Brd4 clone 7 cells also contain bi-allelic integrations of SNAP-tag at the Brd4 locus39 (link). mESC lines for imaging the Sox2 locus were derived from B6 albino mESCs (B6(Cg)-Tyrc-2J/J, Jackson Lab 000058; male - species/sex verified by karyotyping, no additional cell line authentification performed). All cell lines tested negative for mycoplasma.