Extended Data Fig. 3: The segregation of germ-layer tissues by the regulon and transcriptome.
From: Molecular architecture of lineage allocation and tissue organization in early mouse embryo
a, The workflow of regulon analysis in the SCENIC pipeline. Tissue samples from embryos at E2.5 to E7.5 were collated for mining the co-expression genes, cis-regulatory motif analysis and building of regulon units comprising of transcription factors (TF) and targets (TG), and the regulon-activity matrix for each sample were used in subsequent bioinformatic analysis (Methods). Dim, dimension. Transcriptome data of blastomeres of the morula, inner cell mass of the blastocyst and the primitive endoderm and epiblast of E4.5 embryo were sourced from ArrayExpress accession numbers E-MTAB-2958 and E-MTAB-2959. b, Corn plots show the spatial domain of the cell populations of each branch of the phylogenetic tree at E5.5–E7.5. c, t-SNE plots of tissue samples from E5.5 to E7.5 based on gene expression and the regulon-activity matrix (n = 214). d, e, PCA and t-SNE analysis for regulon-activity scores in the epiblast–ectoderm and mesoderm (n = 145) (d) and the primitive streak, mesoderm and endoderm of E5.5 to E7.5 embryos (n = 122) (e). f, Hierarchical clustering analysis for the posterior epiblast/primitive streak, the mesoderm and the endoderm for embryonic samples from E5.5 to E7.5 stages. g, The regulon-activity heat map for primitive streak, mesoderm and endoderm of E5.5 to E7.5 embryo. Sample in each column was ordered based on f, and examples of regulon transcription factors were listed. Regulon transcription factors coloured red were experimentally tested in this study. h, Corn plots showing the pattern of averaged activities of regulon groups in the endoderm, mesoderm and primitive streak samples.
