Extended Data Fig. 2: Transcriptional profiling of L- and D-EPSCs related to Fig. 1.
From: Evaluating totipotency using criteria of increasing stringency
a, Number of DEGs between 2iLif ESCs and L-EPSCs at different days of conversion. b, Gene expression comparison of pluripotency and somatic genes between 2iLif ESCs and L-EPSCs and mouse embryonic fibroblasts (MEFs) as control. 1 sample. c, Changes in expression levels between 2iLif ESCs and L-EPSCs for genes reported to change in Yang et al.35. 1 sample. d, GSEA analysis of 4-cell stage signature genes in bulk RNA-seq data of L-EPSCs generated in this study (2iLif n = 1, EPSC n = 5) and published bulk L-EPSCs RNA-seq data (Yang et al. 35, (2iLif n = 5, EPSC n = 5), Yang et al.36 (2iLif n = 2, EPSC n = 2)). e, UMAP from Fig. 1e showing the resource from which each cell was merged, and lists the number of cells used from each. f, FeaturePlots projecting expression of representative 2-cell, EPI, PE, and TE marker genes, overlaying Fig. 1e UMAP. g, GSEA analysis of 4-cell stage signature genes in scRNA-seq data of L-EPSCs and D-EPSCs generated in this study (2iLif n = 191, L-EPSCs n = 182, D-EPSCs n = 186) and published L-EPSCs scRNA-seq data (Yang et al.35 (2iLif n = 96, EPSC=96)). *: p-value 0,05-0,01, **: p-value 0,01-0,001. h, Heatmap of genes previously reported to be upregulated in D-EPSCs compared to ESCs cultured in Lif/serum conditions, which are similarly upregulated in D-EPSCs (generated in this study) when compared to naïve 2iLif ESCs. i, Violin plot using Module A & B from Yang Y. et al., 2017, Figure 7C36 Fig. 7c, showing significant upregulation in both L-EPSCs and D-EPSCs compared to 2i. N = number of cells in each condition.
