Extended Data Fig. 9: FACS sorting strategy.

(a) Surface marker rankings identified by COMET for the EPCAM+ ectoderm or the (b) PDGFRA+ mesoderm after 7 days of RA/BMP4. Markers used for further analyses are noted in red, and markers that were tested but did not work well by FACS are noted in blue. (c) Expression patterns and fold changes in day 7 scRNA-seq of markers used for cell sorting including VTCN1 (ectoderm), (d) ABCG2 (ectoderm), and (e) PDGFRA (mesoderm). (f) Fluorescence associated cell sorting (FACS) strategy used to separate day 7 cells into ectoderm and mesoderm. Plots show a distinction between ABCG2+ or PDGFRA+ populations or (g) overlapping ABCG2+ and VTCN1+ populations. Populations were gated on unstained control cells, and the gating strategy can be found in the Supplementary Figure 2.