Fig. 1: Generation and analysis of a combined human sequencing dataset.
From: Distinct pathways drive anterior hypoblast specification in the implanting human embryo
a, Diagram depicting human development from blastocyst through pre-gastrulation stages. The datasets integrated to generate our combined object are presented below. b, Uniform manifold approximation projection (UMAP) of datasets coloured by original publication. N = 9,862 single cells. c, UMAP of human datasets coloured by embryo age. d, UMAPs of human datasets coloured by a gradient of canonical marker gene expression for epiblast (EPI), hypoblast (HYPO), trophectoderm/trophoblast (TE/TrB) and terminal extravillous trophoblast (EVT) or syncytiotrophoblast (STB) lineages. e, UMAP coloured by assigned cell type. f, Heatmap of WikiPathways signalling pathway module score for each developmental stage of each individual cell type. Visualized value is calculated average scaled score from individual single-cell module scores. g,h, CellPhoneDB dotplots for blastocyst (g) and peri-implantation (h) stages depicting predicted activity of individual receptor–ligand pairs. Each ligand–receptor pair is colour matched to the expressing lineage on the x axis. N = 9,862 single cells. AP, anterior-posterior; dep, dependent; ind, independent; reg, regulation; comp, complex.
