Extended Data Fig. 5 |. CUT&RUN of pluripotency TFs in SL versus 2i culture conditions.

a, Heatmaps (bottom) and average plots (top) comparing pluripotency TF occupancy by CUT&RUN at RNAPII-enriched (active) and H3K27me3-enriched (bivalent) promoters. Promoters were grouped based on K-means clustering of RNAPII-S5P and H3K27me3 CUT&Tag reads mapping to a 5 kb window around the TSSs of RefSeq-annotated mESC genes, see Extended Data Fig. 4a. b, Immunofluorescent staining comparing pluripotency TF and BRG1 expression in SL versus 2i culture conditions. Cy5-conjugated secondary antibodies were used in all experiment except for KLF4, where Rhodamine red-conjugated antibody was used. DAPI (blue) was used to stain the nucleus in cells. c, Heatmaps (bottom) and average plots (top) comparing pluripotency TF occupancy by spike-in calibrated CUT&RUN in SL versus 2i culture conditions.