Extended Data Fig. 14: Dynamics of gene expression during the 8CLC conversion.
From: Rolling back human pluripotent stem cells to an eight-cell embryo-like stage
a. Hierarchical clustering of 1,497 variable genes among the indicated scRNA-seq (droplet based) samples along the pseudotime of stepwise e4CL induction of 8CLC from primed ESC identifies five gene groups. k = 5. b. Line plots showing the mean standardized gene score of the indicated scATAC-seq samples for each gene group of panel a. 8CLC (cluster 2) and non-8CLC (all other clusters summed) are based on Fig. 2a. The red line represents the median values for the group center. c. Enriched GO terms for biological processes in each of the five groups of panel a relative to all other gene groups. P value was calculated using hypergeometric test and adjusted for multiple testing using Benjamini-Hochberg correction. d. Pseudotime showing the expression pattern of the indicated genes for each cluster of panel a during the stepwise e4CL induction of 8CLC from primed ESC. e. Pseudotime showing the expression pattern of the same genes of panel d during early human embryonic development26. blast., blastocyst. All reference datasets used in this study are summarized in Supplementary Table 8. f. Hierarchical clustering of variable genes among the indicated scRNA-seq samples along the pseudotime of direct e4CL induction of 8CLC from primed ESC identifies five groups. k = 5. Each transcript expression is shown as a gray line; the black line represents the mean expression. g. Pseudotime showing the expression pattern of the indicated genes for each cluster of panel f during the direct e4CL induction of 8CLC from primed ESC. h. Enriched GO terms for biological processes in each of the five groups of panel f relative to all other gene clusters. P value was calculated using hypergeometric test and adjusted for multiple testing using Benjamini-Hochberg correction.
