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. 2024 Jan 5;31(3):498–512. doi: 10.1038/s41594-023-01181-7

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© The Author(s) 2024

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. 2 — (a) Distribution of DNA methylation for Vehicle and Decitabine-treated (n = 4 biological replicates each) Gar15-13 PDXs for EPIC probes located at TAMR ChromHMM enhancer regions. Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test. (b) Distribution of DNA methylation for Vehicle and Decitabine-treated (n = 4 biological replicates each) HCI-005 PDXs for EPIC probes located at TAMR ChromHMM enhancer regions. Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test. (c) Distribution of DNA methylation for Vehicle and Decitabine-treated (n = 4 biological replicates each) Gar15-13 PDXs for EPIC probes located at TAMR ChromHMM promoter regions. Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test. (d) Distribution of DNA methylation for Vehicle and Decitabine-treated (n = 4 biological replicates each) HCI-005 for EPIC probes located at TAMR ChromHMM promoter regions. Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test. (e) H3K27ac CUT&RUN heatmap at H3K27ac binding sites gained and lost in Decitabine compared to Vehicle-treated Gar15-13 PDXs. (f) RefSeq annotation of Vehicle vs. Decitabine common, gained and lost H3K27ac binding sites in Gar15-13. (g) Distribution of DNA methylation for Vehicle and Decitabine-treated (n = 4 biological replicates each) Gar15-13 PDXs for EPIC probes mapping to LTR, LINE1 and Alu elements (REMP annotation). Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test. (h) Distribution of DNA methylation for Vehicle and Decitabine-treated HCI-005 PDXs for EPIC probes mapping to LTR, LINE1 and Alu elements (REMP annotation) (n = 4 biological replicates each). Black line indicates median ± SD. Box plots show median, inter-quartile range and maximum/minimum DNA methylation. Data analysed using the two-sided Z test.