Figure S3.

Temporal Mapping of scRNA-Seq Data, Related to Figure 3

(A) Average linkage hierarchical clustering of gene expression profiles of the 5 cell types at 16-cell stage (blue: A5.1-2, B5.1, B5.2, a5.3-4, b5.3-4) and the 8 cell types at 32-cell stage (red: A6.1&3, A6.2&4, B6.1, B6.2, B6.3, B6.4, a6.5-8, b6.5-8) determined by scRNA-Seq. Actual mother-daughter relationships are indicated by brackets under the cell type names. Number of cells belonging to each cell type in canonical embryos are indicated under the cell type names.

(B) Average linkage hierarchical clustering of gene expression profiles of the 8 cell types at 32-cell stage (red: A6.1&3, A6.2&4, B6.1, B6.2, B6.3, B6.4, a6.5-8, b6.5-8) and the 18 cell types at 64-cell stage (purple: A7.1-2, A7.3&7, A7.4, A7.5, A7.6, A7.8, B7.1, B7.2, B7.3, B7.4, B7.5, B7.6, B7.7, B7.8, a7.9-10, a7.11-16, b7.9, b7.10, b7.11-16) determined by scRNA-Seq. Actual mother-daughter relationships are indicated by brackets underneath the cell type names. Number of cells belonging to each cell type in canonical embryos are indicated underneath the cell type names.

(C) Comparison between expression levels of the five mother cell types at 16-cell stage and their respective daughter cell types at 32-cell stage (blue) or the other cell types (red) found in 32-cell embryos.

(D, E) Projection of single-cell gene expression profiles of individual 16- (D) and 32-cell (E) embryos on the classifier that distinguishes vegetal pole cells form animal pole cells at the 16-cell stage.

(F, G) Projection of gene expression profiles of single animal pole cells of individual 16- (F) and 32-cell (G) embryos on the classifier that distinguishes the two animal pole cell types at the 16-cell stage.

(H) Lineage of P. mammillata up to the 64-cell stage.

(I) Temporal evolution of the number of cells in a P. mammillata embryo up to the 64-cell stage. Horizontal dashed lines indicate 24 and 44 cells.