Fig. 3: Single cell analyses of forelimb histogenesis.
From: The changing mouse embryo transcriptome at whole tissue and single-cell resolution
a, Two-dimensional t-SNE of cell clusters, of 10x (left, n = 90,637 cells) and C1 data (right, n = 920 cells). Colours indicate provisional cell identities as in Supplementary Note 2. b, Cell cluster marker genes (top 15 per cluster), down-sampled for display to 100 cells per cluster for 10x and 30 cells for C1 data. Mes., mesenchymal; Myogen, myogenesis; Skeleto., skeletogenesis; Haemato., haematopoiesis; Ecto, ectoderm; Mus. 1–3, muscle 1–3; Peri, perichondrium; Chon., chondrocytes; NC, neural crest; EE, endothelium and EMP; Ma, macrophage; Ep, epithelium. c, Integrated visualization of 10x (left) and C1 (right) single cells on a 2D UMAP plane, separately or jointly projected (centre; see text and Methods). d, Limb development schematic (arrow indicates immigrating lineages) and cell type composition plotted as a time series. The colour code corresponds to cell clusters in a. e, Monocle lineage inference model for skeletal myogenesis. Pseudotime, developmental time and cell type (left); informative marker gene expression mapped on the right. n = 7,668 muscle cells. f, Box plots of Boolean, graded, and pan-lineage pattern TFs; n = 23 muscle 3 cells; n = 38 muscle 2 cells; n = 54 muscle 1 cells. Boxes, 25th–75th percentiles; centre, median; whiskers, 1.5 × interquartile range.
