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. 2023 Sep 20;14:5830. doi: 10.1038/s41467-023-41418-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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a scRNA-seq-generated UMAP plots of ECs distinguishing four individual subpopulations (left) and tissue sources (right). b Violin plots displaying the expression of representative well-known marker genes across four EC subpopulations. The y-axis represents log-scaled normalized UMI counts. c The proportion of four EC subpopulations of H-MAT, CD-MAT and CF estimated by Ro/e score. d Immunohistochemical staining of CA4 expression in the H-MAT and CF vasculature (representative of 5 BRs per group). Scale bars, 25 μM. e Boxplots comparing the scores of angiogenesis and leucocyte transendothelial migration in EC1 of H-MAT (n = 2), CD-MAT (n = 3) and CF (n = 6). The centre line represents the median, box hinges represent frst and third quartiles and whiskers represent ± 1.5x interquartile range. f UMAP plot of EC1 distinguishing two individual subsets. g Expression levels of representative marker genes for EC1-S1 and EC1-S2 are plotted onto the UMAP. h Monocle analysis of the EC1 subsets indicating pseudotime directionality (bottom left) and cell type; EC1-S1 (blue) and EC1-S2 (cyan). i The differentially expressed genes (rows) along the pseudotime (columns) are clustered hierarchically into two profiles. Heatmap showing the expression of representative TFs in two profiles across single cells. j Bubble plots showing ligand–receptor pairs between EC1s and other cell groups in CD patients and control subjects. The circle size represents the log-normalized P value, whereas the colour represents the log-transformed mean expression of ligand and receptor. k Immunofluorescence confirmed the existence and distribution of pericytes in H-MAT, CD-MAT and CF (representative of 5 BRs per group). Scale bars, 50 μM. e, j Data were analysed using two-sided Wilcoxon rank sum test. Source data are provided as a Source data file.