Validation of STAG2 inactivation, clustering of KT and KT;Stag2 ^flox samples, gene expression of surfactant genes, and differential accessibility regulated by STAG2. (a) Schematic of tumor initiation with Adeno-Spc-Cre with different viral titers in KT and KT;Stag2^flox mice to generate tumor samples to analyze at 8 and 16 wk after tumor initiation. (b) Lung weights of mice in each group. Each dot represents a mouse and the bar is the mean. (c) Number of DNA nucleotide counts at Chromosome X locus in Exon 8 of STAG2 in each group. Note that this region is within floxed exon. Mean ± SEM is shown. (d)Stag2 RNA expression in TPM via RNA-seq in each group. Bar is the standard error. Mean ± SEM is shown. (e) PCA of KT;Stag2^flox and KT tumors processed with RNA-seq libraries at 8 and 16 wk clustered by genotype. (f and g) Gene expression (TPM) for Nkx2-1 (f) and Sftpc (g) for KT and KT;Stag2^flox 8 and 16 wk. **P value <0.01, *P value <0.1 by unpaired t test. Each dot represents a mouse, and the bar is the mean. (h) Quantification of NKX2-1 expression in KT;Stag2^flox (n = 2 mice) and KT (n = 2 mice) tumors at 8 wk after initiation. Tumor NKX2-1 expression quantified by comparison to NKX2-1 expression in adjacent normal tissue. Tumor number quantified labeled in graph. Mean ± SD is shown (P value <0.001 by ordinary one-way ANOVA). (i) PCA of KT and KT;Stag2^flox tumors processed with ATAC-seq libraries at 16 wk clustered by genotype. (j) ATAC-seq signal tracks for the Myct1 gene locus in tumors from KT and KT;Stag2^flox mice. (k) Motif sequences and corresponding P values for transcription factors with motif enrichment in regions with increased accessibility in cancer cells from KT;Stag2^flox mice. (l) Motif sequences and corresponding P values for transcription factors with motif enrichment in regions with decreased accessibility in cancer cells from KT;Stag2^flox mice.