Extended Data Fig. 2: Cell-type assignments based on RNA expression.
From: Multi-omics profiling of mouse gastrulation at single-cell resolution
a, b, Lineage assignment of E4.5 cells (a; n = 175) and E5.5 cells (b; n = 173). Top left, SC3 consensus plots representing the similarity between cells on the basis of averaging of clustering results from multiple combinations of clustering parameters. Top right, heat map showing the RNA expression (log normalized counts) of the ten most informative gene markers for each cluster. Bottom left, t-distributed stochastic neighbour embedding (t-SNE) representation of the RNA-expression data coloured by the expression of Fgf4 and Pou5f1, known E4.5 and E5.5 epiblast markers50,51, respectively. Bottom right, t-SNE representation of the RNA-expression data coloured by the expression of Gata6 and Amn, known E4.5 primitive endoderm and E5.5 visceral endoderm markers52. c, d, Lineage assignment of E6.5 cells (c; n = 977) and E7.5 cells (d; n = 1,155). Left, UMAP projection of the atlas dataset (stages E6.5 to E7.0 to assign E6.5 cells and E7.0 to E8.0 to assign E7.5 cells). In the top-left panel, cells are coloured by lineage assignment. In the bottom-left panel, the cells coloured in red are the nearest neighbours that were used to transfer labels to the scNMT-seq dataset. In right panels, cells are coloured by the relative RNA expression of lineage-marker genes. e, Top, number of cells per lineage, using the maximally resolved cell types reported in ref. 4. Bottom, number of cells per lineage after aggregation of cell types belonging to the same germ layer or extra-embryonic tissue type, as used in this study.
