Fig. 1: Whole-tissue polyA-RNA transcriptome structure with cell-type decomposition.

a, Schematic of E10.5 and E15.5 embryos shows the colour key for organ identity and developmental stage across the timespan of the study with the complete key adjacent and the major cellular mechanisms of histogenesis below. b, Whole-tissue transcriptome top three PCs; colour code from a (viewable in 3D, Supplementary Video 1). n = 156 biological replicates. c, Hierarchical clustering of differentially expressed genes, heat map (bottom) for normalized log₂(FPKM) values; two biological replicates per tissue. Thy, thymus; Spl, spleen; Lvr, liver; Hrt, heart; Mus, skeletal muscle; Bld, bladder; Adr, adrenal gland; Kdn, kidney; Lng, lung; Stm, stomach; Int, intestine; Lmb, limb; Fac, craniofacial prominence; Fb, forebrain; Mb, midbrain; Hb, hindbrain; Nt, Neural tube. Right, normalized loadings of each gene for the top five PCs. Bottom, normalized scores of the top five PCs (same sample order as clustergram). GO terms for the top 100 positive-loading and top 100 negative-loading genes abbreviated as key words (bottom right). Blood, blood microparticle; Neuron, neuron part; Embryo, embryonic morphogenesis; Extracell., extracellular region part; Cycle, mitotic cell cycle process; Digestive, digestive system process; Contract, contractile fibre part; Intestinal, intestinal epithelial cell differentiation; Skel. mus., skeletal muscle contraction. d, Integrating single-cell organogenesis data from whole mouse embryos¹¹ with the whole-tissue transcriptome clustering (c). y-axis, genes are ordered as in c; x-axis, 38 cell types from ref. ¹¹. A point in the diagram indicates expression of a marker gene from ref. ¹¹ with horizontal jittering. Boxes highlight specific cell types and gene clusters of interest (see text).