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. 2023 Jan 19;55(2):232–245. doi: 10.1038/s41588-022-01280-z

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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. 10 — a-d. RNA-seq analysis of Notch1^+/+ and Notch1^−/− esophageal tissue and tumors, see Fig. 8a. a. Principal component analysis (PCA) plot showing in two dimensions all biological replicates from Notch1^+/+ normal epithelium (n = 11 biopsies from 7 mice, green), tumors from Notch1^+/+ epithelium (n = 8 tumors from 4 mice, red), Notch1^−/− normal epithelium (n = 10 biopsies from 7 mice, blue) and tumors from Notch1^−/− epithelium (n = 6 tumors from 5 mice, orange). Dotted lines indicate the origin of the axes. b. Hierarchical clustering and heat map showing differentially expressed genes between tumors and adjacent normal tissue, in Notch1^+/+ mice (left) and Notch1^−/− mice (right). c. Hierarchical clustering and heat map showing differentially expressed genes between tumors from Notch1^+/+ and Notch1^−/− esophagus. d. Gene Set Enrichment Analysis (GSEA) of tumors from Notch1^−/− vs Notch1^+/+esophagus. Normalized enrichment score (NES) of altered Biological Process gene sets in tumors. False discovery rate, FDR q-value<0.05. e. Representative images of n = 8 tumors from Notch1^+/+ and n = 9 tumors from Notch1^−/− esophagus. KRT14 (green), CCNB1 (magenta). DNA, blue. Scale bars, 30 µm. f. Percentage of CCNB1 positive; KRT14 expressing keratinocytes within tumors from Notch1^+/+ and Notch1^−/− esophagus. Mean ± SEM, each dot represents a tumor, +/+: n = 8 tumors from 4 mice; −/−: n = 9 tumors from 7 mice. Two-tailed unpaired Student’s t-test. See Supplementary Tables 24 and 27–29.