Extended Data Fig. 2: LKB1 restoration drives widespread changes in chromatin accessibility in lung adenocarcinoma cells.

a. Schematic of preparing LKB1-deficient and LKB1-restored samples prior to ATAC-seq library preparation. Cell lines were treated with 4-OHT or vehicle for six days. b. Representative plot of aggregate signal around the transcription start site (TSS) for all ATAC-seq peaks in one vehicle-treated, LR1 replicate. This plot represents the signal-to-noise quantification of our ATAC-seq data. TSS enrichment scores greater than 10 indicate high quality ATAC-seq data. c. TSS enrichment scores for 16 ATAC-seq libraries with technical replicates. d. Differential accessibility across 178,783 ATAC-seq peaks following 4-OHT treatment in the LKB1-restorable (LR1 and LR2) and LKB1-unrestorable (LU1 and LU2) cell lines. The x-axis represents the log₂ mean accessibility per peak and the y-axis represents the log₂ fold change in accessibility following 4-OHT treatment. Colored points are significant (|log₂ fold change | >0.5, FDR < 0.05). e. Percentage of differential peaks (|log₂ fold change | >0.5, FDR < 0.05) across multiple ATAC-seq comparisons. f. Schematic of preparing samples for LKB1-restoration time-course. Cell lines were treated with 4-OHT for eight different time-points (0 hours, 6 hours, 12 hours, 24 hours, 36 hours, 48 hours, 4 days, and 6 days) in two cell lines (LR1 and LR2). g. and h. PCA (g) and k-means clustering (h) of 9,480 correlated, variable ATAC-seq peaks across the LKB1 restoration time-course in two cell lines (LR1 and LR2). Each row of the heatmap represents a z-score of log₂ normalized accessibility across all samples within each cell line. i and j. SOX (i) and TEAD (j) motif accessibility changes (∆chromVAR deviation scores) across time in two cell lines (LR1 and LR2) treated with 4-OHT for the indicated time-points. Shaded area represents 95th percent confidence interval.