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. 2023 Jun 16;14:3599. doi: 10.1038/s41467-023-39347-y

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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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Fig. 7 — a Experimental design for the comparison of spheroids against monolayer culture of HCT116 cancer cells treated with 5-Fluorouracil. b Heatmap showing the phosphosites from the SureQuant™ Multipathway Phosphopeptide Standard panel that are differentially regulated (two-sided two-samples t-test, BH-FDR) in at least one point. Color indicates the average log2 fold change of each time point against time 0 (n = 5 biological replicates). Asterisk indicates q-value < 0.05. c Boxplot of MS2 intensities obtained from hybrid-DIA scans of relevant phosphorylation markers of DNA damage (n = 5 biological replicates) in single spheroids or monolayer grown cells. Intensities are not normalized by loading amount between spheroids and monolayer cells. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. Source data are provided as a Source Data file.