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. 2024 Jan 3;15:210. doi: 10.1038/s41467-023-44645-6

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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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Fig. 4 — a UMAP plot showing 5070 endothelial cells colored by sub-clusters. b UMAP plot showing the endothelial cells colored by disease conditions. c Dot plot showing the top marker genes for each endothelial sub-cluster. The color scale represents the scaled expression of each gene. The size of the dot represents the percentage of cells expressing the gene of interest. d Violin plots showing the expression level of representative genes in the endothelial sub-cluster 0, 1 and 2. e Violin plots showing the extracellular matrix module score in the endothelial sub-clusters. f UMAP plot showing the CytoTRACE score in the endothelial sub-clusters. A higher CytoTRACE score suggests the cell being more differentiated. g Immunofluorescence showing the colocalization of SMA and CD31 in the NS and SSc skin tissues. Images shown are representative of n = 3. The size bar represents 20 μm. h Pseudotime trajectory colored by the pseudotime (left) and sub-cluster identity (right) of three endothelial sub-clusters. i Scatter plot showing the correlation coefficients between the target score of the upstream regulators and the fibroblast pseudotime (X axis) and endothelial pseudotime (Y axis). j Immunofluorescence showing the colocalization of TEAD1/CD31 (left) and TEAD3/CD31 (right) in the NS and SSc skin tissues. Images shown are representative of n = 3. The size bar represents 20 μm. k Bar plots showing the percentage of cells expressing the gene in the endothelial sub-cluster 0, 1 and 2. l Bar plot showing the top five Gene Ontology pathways enriched for the 240 common up-regulated genes in fibroblast group 3 compared to group 1, 2 and endothelial sub-cluster 2 compared to sub-cluster 0, 1.