Related to Fig. 2. a–d, Cluster annotation based on the expression levels of conventional lineage markers. Each dot represents a single cell, and the cells are coloured based on the expression levels (log2(TPM + 1)) of several known gene markers for specific lineages. For example, the EPI population expressed the key pluripotency markers POU5F1 (encoding OCT4), NANOG and SOX2. a–c, Colours from yellow to red represent expression levels from low to high. d, The violin plots show the expression of OTX2 in three main lineages; by setting scale = width, all violins have the same maximum width. In total, 5,911 cells were included; EPI, n = 330; PE, n = 179; TE, n = 5,363; ysTE, n = 39. e, The expression levels of conventional lineage markers at single-cell levels. The cells that clustered away from the other three main cell clusters showed high expression of TE markers (for example, GATA3) and low expression of EPI (for example, SOX2) and PE (for example, GATA4) markers. Colours from blue to red represent expression levels from low to high.