a, Cluster 0 peaks have higher FOXA1 ChIP–seq signal in F254_E255del mutant organoid than empty vector control. Box plots show normalized day five AR ChIP–seq signal and FOXA1 ChIP–seq signal across different organoid lines at peaks from cluster 0, where normalization is based on background ChIP signal. FOXA1 ChIP signal is significantly higher in F254_E255del (FE) and in WT compared to EV control (P values are listed in Supplementary Table 11). Sample size = 5,260 peaks. b, Cluster 1 peaks have higher FOXA1 ChIP–seq signal and lower AR ChIP–seq signal in FOXA1(WT)-overexpressing organoids than in EV control. Box plots show normalized day five AR ChIP–seq signal and FOXA1 ChIP–seq signal across different organoid lines at peaks from cluster 1, where normalization is based on background ChIP signal. FOXA1 ChIP signal is significantly higher, and AR ChIP signal significantly lower, in WT compared to EV control. Sample size = 1,493 peaks. c, Cluster 3 peaks have higher FOXA1 ChIP–seq signal in R219S organoid than EV control. Box plots show normalized day five AR ChIP–seq signal and FOXA1 ChIP–seq signal across different organoid lines at peaks from cluster 3, where normalization is based on background ChIP signal. FOXA1 ChIP signal is significantly higher in R219S compared to EV control. Sample size = 6,641 peaks. d, Cluster 5 peaks have higher FOXA1 ChIP–seq signal and lower AR ChIP–seq signal in R219S organoid than EV control. Box plots show normalized day five AR ChIP–seq signal and FOXA1 ChIP–seq signal across different organoid lines at peaks from cluster 5, where normalization is based on background ChIP signal. FOXA1 ChIP signal is significantly higher, and AR ChIP signal significantly lower, in R219S compared to EV control. Sample size = 1,983 peaks. In a–d, box: 25th to 75th percentile; band: median; top whisker: 75th percentile plus 1.5 times interquartile range; bottom whisker: 25th percentile minus 1.5 times interquartile range. P values calculated using an unpaired, one-sided Wilcoxon test. e, Genes associated with cluster 0 are significantly induced in F254_E255del mutant organoids. Top, plots show empirical cumulative distribution of log 2 expression changes at 24 h vs day 0 in WT (left), F254_E255del mutant (middle) and R219S mutant (right) organoids for all expressed genes (black), genes associated with at least one ATAC-seq peak in cluster 0 (cluster 0-associated genes, red), and the top quartile of these genes based on number of assigned cluster 0 peaks (strong cluster 0-associated genes, yellow). Cluster 0-associated genes show strong expression induction compared to all genes in F254_E255del as well as in WT (red vs black) but not in R219. Bottom, As a control, similar cumulative log 2 expression changes for cluster 1-associated genes (red) or strong cluster 1-associated genes (yellow) do not show significant induction in F254_E255del. All P values are listed in Supplementary Table 12 and are one-sided Wilcoxon rank-sum tests. f, Genes associated with cluster 0 are significantly induced in F254–E255del mutant organoids. Top, plots show empirical cumulative distribution of log 2 expression changes at 11 days vs day 0 in WT (left), F254_E255del mutant (middle) and R219S mutant (right) organoids for all expressed genes (black), genes associated with at least one ATAC-seq peak in cluster 0 (cluster 0-associated genes, red), and the top quartile of these genes based on number of assigned cluster 0 peaks (strong cluster 0-associated genes, yellow). Cluster 0-associated genes show strong expression induction compared to all genes in F254_E255del as well as in WT but not in R219. Bottom, As a control, similar cumulative log 2 expression changes for cluster 1-associated genes (red) or strong cluster 1-associated genes (yellow) do not show significant induction in F254_E255del. All P values are listed in Supplementary Table 12 and are one-sided Wilcoxon rank-sum tests. g, Genes associated with clusters 3 and 5 are significantly induced in R219S mutant organoid. Top, plots show empirical cumulative distribution of log 2 expression changes at 24 h vs day 0 in WT (left), F254_E255del mutant (middle) and R219S mutant (right) organoids for all expressed genes (black), genes associated with at least one ATAC-seq peak in cluster 3 (cluster 3-associated genes, red), and the top quartile of these genes based on number of assigned cluster 0 peaks (strong cluster 3-associated genes, yellow). Cluster 3-associated genes show strong expression induction compared to all genes in R219S but not in WT or F254_E255del. Bottom, similar analysis for cumulative log 2 expression changes for cluster 5-associated genes (red) and strong cluster 5-associated genes (yellow). These genes are significantly induced in R219S and repressed in F254_E255del in WT for this time point. All P values are listed in Supplementary Table 12 and are one-sided Wilcoxon rank-sum tests. h, Genes associated with clusters 3 and 5 are significantly induced in R219S mutant organoid. Top, Plots show empirical cumulative distribution of log 2 expression changes at day 11 vs day 0 in WT (left), F254_E255del mutant (middle) and R219S mutant (right) organoids for all expressed genes (black), genes associated with at least one ATAC-seq peak in cluster 3 (cluster 3-associated genes, red), and the top quartile of these genes based on number of assigned cluster 0 peaks (strong cluster 3-associated genes, yellow). Cluster 3-associated genes show strong expression induction compared to all genes in R219S but not in WT or F254_E255del. Bottom, similar analysis for cumulative log 2 expression changes for cluster 5-associated genes (red) and strong cluster 5-associated genes (yellow). These genes are significantly induced in R219S and repressed in F254_E255del. All P values are listed in Supplementary Table 12 and are one-sided Wilcoxon rank-sum tests. Source data Source data