Extended Data Fig. 4: ATAC-seq analysis of AV cells and tumor cells.

a, Differentially accessible chromatin regions identified between Gp1-WT-like AV cells and Gp2-HET AV cells (top, more open in Gp2 than Gp1, Gp1 < Gp2; bottom, more closed in Gp2 than Gp1, Gp1 > Gp2) are further categorized by differential accessibility between Gp2-HET AV cells and Gp3-tumor cells. ‘Progressively open’ regions (that is Gp1 < Gp2 < Gp3 and Gp1 < Gp2 ~ Gp3) and ‘progressively closed’ regions (that is Gp1 > Gp2 > Gp3 and Gp1 > Gp2 ~ Gp3) are highlighted. b, Stacked bar graph of distance to transcription start site (TSS) for progressively altered chromatin regions identified between Gp1 vs Gp2 vs Gp3 cells. c, Proportion of genes associated with the indicated differentially accessible chromatin regions in ATAC-seq (that is genes with coding regions located within 10 kb or those with the nearest TSS) that exhibit a higher, lower, or not significantly different expression level in tumor cells relative to AV cells by scRNA-seq. In both groups (Gp1 < Gp2 and Gp1 > Gp2), and for both gene association approaches (within 10 kb or nearest TSS), p = 4.89E-36 (Fisher’s exact test). d, Percent of genes associated with the indicated open or closed chromatin regions in ATAC-seq (that is genes with coding regions located within 10 kb or those with the nearest TSS) that exhibit a higher or lower expression level in tumor cells relative to AV cells in scRNA-seq analysis, respectively. For Tumor > AV (Gp1 < Gp2 vs Gp1 < Gp2 < /~Gp3), p = 1.10E-06 (within 10 kb) or 3.38E-05 (nearest TSS); for Tumor < AV (Gp1 > Gp2 vs Gp1 > Gp2 > /~Gp3), p = 8.30E-05 (within 10 kb) or 1.92E-05 (nearest TSS) (Fisher’s exact test, two-sided).