Fig. 5: PrE signatures during the primed-to-naive transition.

a ATAC-seq tracks showing the chromatin landscape of representative PrE-related genes in intermediate cells during the primed-to-naive transition. b MAplot of bulk RNA-seq datasets for comparing SSEA4⁻ cells with SSEA4⁺ cells on day 6 during the primed-to-naive transition with the differentially expressed (DE) genes highlighted. |log2FC | ≥ 1, adjusted p value < 0.01 (n = 3 biologically independent samples). c Expression of POSTN and SERPINH1 (marker gene of the PrE layer) as determined by FDL. d Experimental design for the induction of embryonic endoderm cell lines from the primed-to-naive intermediates following the reported protocol³⁸. e Representative images (upper panels) and immunostaining (lower panels) showing the morphologies and GATA6 expression of endoderm cell lines derived from day6-SSEA4⁻ cells, day 6-SSEA4⁺ cells, day8 RFP- cells, day8 RFP⁺ cells, pESCs and nESCs. Scale bar (upper panels 50 μm, lower panels 20 μm). Representative images from n = 3. f Heatmap to indicate the samples distance among bulk RNA-seq datasets of endoderm cell lines derived from day6-SSEA4⁻ cells, day 6-SSEA4⁺ cells, day8 RFP- cells, day8 RFP⁺ cells, pESCs and nESCs with published RNA-seq datasets³⁴, n ≥ 2. g Heatmap showing the expression levels of representative DE and PrE-related genes of endoderm cell lines derived from day6-SSEA4⁻ cells, day 6-SSEA4⁺ cells, day8 RFP- cells, day8 RFP⁺ cells, pESCs, nESCs and published endoderm cells³⁴. Source data are provided as a Source Data file.