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. 2023 Apr 10;8(5):875–888. doi: 10.1038/s41564-023-01346-6

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 9 — (A-B) HOMER motif analysis of ATAC-seq data in Fig. 4 was performed to show differential TF binding motif enrichment in the DARs found in Sensitized and Resolved USCs. Using a list of each top 10 known and de novo motifs of Sensitized-accessible DARs (A) and Resolved-accessible DARs (B) (Extended Data Fig. 3a, b), differential gene expressions of these motif binding TFs in Naïve, Resolved, and Sensitized differentiated urothelia are visualized as heatmaps. Genes that are not found in RNA-seq data are excluded from the heatmap. (C) Top 10 differentially expressed TFs between Sensitized vs. Resolved differentiated urothelia are visualized as a heatmap with Log₂(FC) and P-adj indicated. Significance of DEGs was determined by Wald test followed by multiple test correction using Benjamini-Hochberg FDR for adjusted p-value.