(A and B) ES cells were placed under neural differentiation conditions. 40–80 single cells were analysed by qRT-PCR from the starting population (Day 0) or at daily time points during differentiation. A shows expression levels of Cdh1, Cdh2, Oct4 and Sox1 in single cells analysed at day 3 of differentiation. The expression values for each factor are normalised to the maximum expression level found in this set of cells. The samples are sorted in ascending order of Cdh1 expression. B shows the Spearman’s rank correlation coefficients (ρ) between the named genes and Cdh1 at each time point. * indicates asymptotic p value <0.05. (C) Oct4 and Cdh1 staining in 7 µm sections of embryos at E7.5 (late streak stage) or staged according to number of somite pairs (s) as indicated. Top row shows bright field images of embryos before sectioning with a white line indicating the location of the section shown in the bottom row. Scale bars = 100 μm. NT: Neural tube (Yellow region in later stage embryos), SE: Surface ectoderm (red region in later embryos). (D) Quantification of the average intensities of Oct4 and Cdh1 in different structures of the embryo at each stage. EPI: Epiblast (yellow region and red region in LS embryo), Error bars represent the standard deviation of intensities in three different sections. Abbreviations are as described for C. (E) Sox1-GFP ES cells after 4 days in neural differentiation conditions stained for Cdh1 (red) and DAPI (blue) with Sox1-GFP in green. Scale bar = 30 μm. (F) E14tg2α ES cells after 4 days under neural differentiation conditions stained for Cdh1 (red) Keratin8 (blue) and Oct4 (green).Scale bar = 30 μm.