Fig. 2.

Cell-type identification and trajectories in a temporal scRNA-seq atlas of development in He. (A) UMAP plot that projects the gene expression profiles of each cell into two-dimensional space, colored by sample time point. (B) UMAP that colors each cell by its cell type identity based on the expression of known cell-type marker genes. (C-H) HCR micrographs in 56 hpf He larvae for six marker genes that were used to identify cell types in the scRNA-seq atlas: pks1, a marker for pigment cells (C); onecut, a marker for the ciliary band (D); foxq2, a marker for the animal pole domain (E); egfi, expressed in the rudiment ectoderm (F); dynlc2, expressed at the tips of the primary podia (G); and hox7, expressed in the posterior ectoderm and inside the rudiment (H). Scale bars: 50 µm.