Extended Data Fig. 4. SOX2 and β-catenin co-occupy differential peaks.

(a) Comparison of SOX2 and β-catenin ChIP-seq peaks identified in data from this study with¹². (b) Our consensus SOX2 and β-catenin peak sets include the majority of those identifiable from the data from¹², plus a large number of additional peaks. (c) Peaks differentially occupied by β-catenin (FDR <0.05) between ES cells and CEpiLCs exhibit a correlated change of SOX2 occupancy. FDR was determined by DESeq2 padj metric from n=3 biological replicates. log2FC calculated by DESeq2. (d) Differentially occupied β-catenin peaks overlap with differentially occupied SOX2 peaks to a greater extent than with peaks occupied by other ENCODE chromatin-associated proteins (ENCODE). Numbers of peaks in each set are show. (e) Metaplots of triplicate SOX2 and (f) β-catenin ChIP-seq signals at cell-type specific SOX2 bound CREs classified in Fig. 3e. Metaplots show mean ± s.e.m.