Extended Data Fig. 4: ONECUT1 shapes chromatin accessibility during PE-PP transition.
a, PCA analysis of stage-specific ATAC-seq for differentiation of ONECUT1 null and WT HUES8 lines (left) as well as restricted to PE and PP stages (right). b, Genomic ___location of stage-specific ATAC peaks lost or gained in ONECUT1 null (KO) HUES8 line. TTS: transcriptional termination site. c, Heatmap depicting chromatin accessibility signals (+/- 2 kb of peak center) of OC peaks lost upon ONECUT1 KO in HUES8 and ordered by ONECUT1 ChIP-seq peak strength at the PE and PP stage. d, Enrichment analysis (GREAT) of OC peaks lost upon ONECUT1 KO at the PE stage. e, Significance of overlap (log10 p-value) of open chromatin (OC) for different tissues as well as OC lost in HUES8 KO at PE or PP stage and ONECUT1 ChIP-seq peaks. f, Scatter plot depicting the footprint-based activity score (strength of binding) of TFs in PE state (y-axis) versus the difference of the activity score upon ONECUT1 KO at the PE state (ATAC-seq, HUES8). g, HNF family factors have the highest loss in activity followed by PAX family, SOX9 and PDX1 factors upon ONECUT1 KO. Representative examples of footprints.
