Fig. 6. Aberrant SOX2 and NANOG activity in the patient cells at CNCC day 5.

a Spike-in normalized SOX2 ChIP-seq average profile for 3284 patient-specific ATAC-seq peaks showing patient-specific SOX2 signal (spike-in normalized; CNCC Day 5). Statistical significance was assessed with Wilcoxon’s Rank-Sum test (p < 2.2 × 10⁻¹⁶ in all the patient vs control comparisons). b ATAC-seq heatmaps at the 3284 peaks shown in Fig. 5a reveal that these regions display increased chromatin accessibility in the patients relative to the two control lines. c ATAC-seq heatmaps at 4538 patient-specific NANOG peaks display no changes in accessibility between patient and control lines. d Spike-in normalized NANOG ChIP-seq heatmaps at 4538 patient-specific NANOG peaks (spike-in normalized; CNCC Day 5). e Example of patient-specific NANOG peak in a region with no chromatin accessibility (CNCC Day 5). f At CNCC Day 5, a cis-regulatory element in the promoter region of NANOG is more accessible in the patients than in the control lines. The same element also displays higher SOX2 binding in the patients than in the controls. g Knockdown of ARID1B from Control Line-1 also elicits an increase in chromatin accessibility at the cis-regulatory element in the promoter region of NANOG (CNCC Day 5).