Fig. 2
mESCs showed gradual adoption and divergence of lineage specific expression profiles. a Principal component analysis of single-cell expression profiles. Principal components were calculated across all cells and time points. Cells measured at the indicated periods of RA exposure were placed in the space of the first two principal components. Each data point corresponds to a single cell. Cells were classified as mESC-like (orange), ectoderm-like (red) and XEN-like (blue). Classification was based on Pearson correlation between expression profiles of individual cells and mean expression profiles of mESCs at 0 h or ectoderm-like and XEN-like cells after 96 h of RA exposure. An individual cell is identified with the cell type with which it is most strongly correlated. b Same data as in a for three select time points (24 h, 36 h and 48 h), zoomed in on the areas indicated by dashed rectangles in a. c Relative frequencies of cells classified as mESC-like, ectoderm- or XEN-like in the same way as in a. d Average movement of ectoderm- and XEN-like cells in the principal component space during RA differentiation. The positions of cells of the same type were averaged at the indicated time points
