“…Joint uniform manifold and projection (UMAPs) and clustering analysis revealed ten distinct cell clusters for all cells within each developmental stage ( Figures 1 B–1E and S1 E–S1H). To annotate the identities of cell clusters, we analyzed the database of known cell lineage markers in bovine, 15 , 16 , 17 , 18 , 19 humans and mouse, 20 , 21 , 22 and selected the markers that were detected in our single-cell transcriptomes of bovine peri-implantation embryos ( Data S1 ). We identified VIM , NANOG, MLY4, SLIT2, ACTA2, COL1A2, and BMP4 as marker genes of embryonic disc (ED), SOX17, GATA4, FST, FN1, CDH2 and CLU as marker genes of hypoblast (HB), and FURIN, IFNT, SFN, DAB2, PAG2 and PTGS2 as trophoblast cell markers ( Figure 1 G).…”