Extended Data Fig. 6: OTX2 over-expression in hESCs.
From: Maternal factor OTX2 regulates human embryonic genome activation and early development
(a) Volcano plot showing DEGs (computed by DESeq2) upon OTX2 OE in primed hESCs. (b) The cumulative curve showing distributions of down-regulated, up-regulated, and all expressed genes upon OTX2 OE with defined distances (x-axis) between their TSSs and nearest OTX2 binding peaks in the OTX2 OE hESCs. P-value, two-sided Kolmogorov–Smirnov test. (c) Left, heatmap showing enrichment of ATAC-seq signals in hESCs before and after OTX2 OE, OTX2 motif densities, OTX2 binding signals in OTX2 OE hESCs and 4C embryos. Right, cumulative curves showing distributions of down-regulated, up-regulated, and all expressed genes upon OTX2 OE in hESCs with defined distances (x-axis) between their TSSs and nearest ATAC-seq peaks. ATAC-seq signals are Z-scored. N, peak numbers. P-values (Kolmogorov–Smirnov test) are shown. (d) Box plots showing RNA changes of genes surrounding the promoter ATAC-seq peaks in (c) upon OTX2 OE. Center line, median; box, 25th and 75th percentiles; whiskers, 1.5 × interquartile range. P-values, two-sided t-test. (e) UCSC browser snapshots showing ATAC-seq signals before and after OE OTX2 in hESCs, OTX2 binding signals in OTX2 OE hESCs, and 4C embryos at targeted genes. mRNA levels are shown in the heatmaps. (f) Venn diagram comparing the OTX2 and TPRX1/2 OE up-regulated genes in primed hESCs and 4C/8C-activated EGA genes. P-values (Fisher’s test) are shown. (g) GO terms for the up-regulated/down-regulated EGA genes upon OTX2 OE in primed hESCs (left) and naïve hESCs (right). (h) Venn diagram showing the OTX2 OE up-regulated genes in primed /naïve hESCs and 4C/8C-activated genes. P-values (Fisher’s test) are shown.
