Extended Data Fig. 7: The tissue spatial domains in the germ layers of E7.5 embryo and endoderm single-cell proportion in the endoderm.
From: Molecular architecture of lineage allocation and tissue organization in early mouse embryo
a, Heat map and corn plots of DEG groups at the E7.5 stage. Representative genes of each DEG group are listed. Corn plots show the spatial domains and the average expression level of the gene group. b, Genes that are specifically expressed in the node region (DEG G5) of E7.5 embryos with high expression values and the corresponding JSD specificity score (in the distal-endoderm domain). c, Top ten (with the highest JSD scores) examples of node-specific expression pattern shown in corn plots. d, The dynamic expression of three E7.5 G5 genes during gastrulation shown in corn plots and compared with WISH results at E7.5 stage. Embryos are oriented with posterior to the right and distal to the bottom (n > 3 for each gene). e, Gene-filter criteria of single-cell RNA-seq data (n = 384 cells; top and bottom of each violin plot represent maxima and minima). Cells with number of detected genes less than 8,000 were discarded (left, red dotted line) and cells with the percentage of reads mapped to mitochondrial genes less than 0.2 were reserved for further analysis (right, red dotted line). f, UMAP plots of 345 single cells (that passed the quality check) in three clusters, indicted by different colours. g, Violin plots of gene-expression level of Sox17 and T across three clusters (SC-C1, n = 213 cells; SC-C2, n = 96 cells; SC-C3, n = 36 cells; top and bottom of each violin plot represent maximum and minimum, respectively). h, Feature plots of represented lineage markers (n = 345 cells). The colour gradient indicates levels of expression.
