Stag2 deficiency impacts overall chromatin looping with effects on gene expression. (a) Schematic of tumor initiation with Adeno-Spc-Cre in KT and KT;Stag2^flox mice. Outline of tumor cell sorting, crosslinking, and sample preparation for Hi-C. (b) Venn diagram of loops in KT and KT;Stag2^flox samples. (c) Venn diagram of loop anchors in KT and KT;Stag2^flox samples. (d) Sizes for KT unique loops, common loops, and KT;Stag2^flox unique loops. Boxes show median ± interquartile range. Whiskers show standard error. P values (Wilcoxon rank test) are shown. (e) Loops in KT and KT;Stag2^flox samples were compared and sorted into indicated categories based on their unique and shared loop anchors. (f) Differences in chromatin looping and gene expression (from RNA-seq data, log₂ fold change [KT;Stag2^flox/KT]; P value) for Ereg and Fgfr2.