KT and KT;Stag2 ^flox samples contain both unique and common DNA loops and DNA anchors that correlate with gene expression but not chromatin accessibility. (a) Normalized contact matrices in KT (top) and KT;Stag2^flox (bottom) neoplastic cells. Contact matrices were visualized in Juicebox with the same color scale. Arrows indicate novel or stronger loop contacts in KT;Stag2^flox. (b) Comparison of loop intensity (log₁₀[observed/expected]) of the indicated loop sizes between all loops in KT and KT;Stag2^flox samples. Boxes show median ± interquartile range. Whiskers show standard error. P values (Wilcoxon rank test) are shown. (c) Change in loop size between the KT;Stag2^flox unqiue loops and the common loops or KT unqiue loops with which they share one anchor (blue). Change in loop size between KT unique loops and the common loops or KT;Stag2^flox unqiue loops with which they share one anchor (orange). (d) Number of genes associated with KT;Stag2^flox unique loops that are upregulated (left) or downregulated (right) in KT;Stag2^flox samples versus all other genes that are and are not associated with KT;Stag2^flox unique loops. P value (chi-square test) is shown. (e) Number of genes associated with KT unique loops that are upregulated (left) or down-regulated (right) in KT samples versus all other genes that are and are not associated with KT unique loops. P value (chi-square test) is shown. (f and g) Differences in chromatin looping and gene expression (from RNA-seq data, log₂ fold change [KT;Stag2^flox/KT]; P value) of several differentially expressed genes proximal to unique anchor sites.