Extended Data Fig. 2: t-SNE projections of ten stages from single-cell RNA-sequencing data.
From: Comprehensive single-cell transcriptome lineages of a proto-vertebrate
a, t-SNE plot of the entire dataset (n = 90,579 cells). Cells are coloured and labelled by clusters. Differentially expressed genes in each cluster can be found in Supplementary Table 2. b, t-SNE plot of all of the cells, coloured according to tissue type. c–l, t-SNE projections of cells, coloured by tissue types at different stages of development (iniG, n = 2,863 cells; midG, n = 3,384 cells; earN, n = 7,154 cells; latN, n = 8,449 cells; iniTI, n = 5,668 cells; earTI, n = 7,109 cells; midTII, n = 8,991 cells; latTI, n = 18,535 cells; latTII, n = 12,635 cells; and larva, n = 15,791 cells). The colour code is the same as in b. m, Violin plots illustrating expression levels of representative marker genes per cell per tissue type (endoderm, n = 14,162 cells; epidermis, n = 26,936 cells; germ cells, n = 396 cells; mesenchyme, n = 19,143 cells; muscle and heart, n = 3,691 cells; nervous system, n = 22,198 cells; and notochord, n = 4,053 cells). Colour code is the same as in b.
