Embryonic stem (ES), trophectoderm (TS) and extra-embryonic endoderm (XEN) cell populations have distinct replication timing profiles, which reflect their lineage potential. (A) Summary of the replication timing comparison of the selected candidate genes between the three embryo-derived stem cell lines. The replication timing of each gene was defined according to its peak abundance in G1/S1 (early, dark green), S2 (middle-early, light green), S2 and S3 (middle, yellow), S3 (middle-late, orange) or S4/G2 (late, red), determined in at least two independent experiments. Inner cell mass/ES-, TE/TS-, PrE/XEN-related loci or genes involved in the specification of somatic cell types are grouped into four different boxes. (B) Histograms comparing the relative abundance of locus-specific signal for Rex1, Sox2, Pem, Pl1, Gata6, Foxa2, Sox1 and Neurod loci within each cell cycle fraction for ES (black bars), TS (white bars) and XEN (grey bars) cells as assessed by quantitative polymerase chain reaction. Mean and standard deviation of two or more experiments are shown for each cell type analysed.