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. 2021 Sep 28;20:124. doi: 10.1186/s12943-021-01419-2

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© The Author(s) 2021

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Characteristics of T cell clusters. A Separate UMAP plots of T cell clusters from skin samples of patients MF309, MF311 and MF312. B UMAP plots of the single top expanded clone (according to the most common α and/or β chain CDR3s aminoacid sequence) per patient. C Combined UMAP of T cell clusters colored according to clonality of TCR. Red: Cells with top expanded monoclonal TCR(s) from each sample; turquoise: cells with polyclonal TCR. D Percentage of monoclonal and polyclonal populations per T cell cluster. E Heat map displaying top differentially expressed genes between expanded clones and polyclonal TCR+ cells, according to the smallest adjusted p-value and average log fold change as calculated by logistic regression with Bonferroni correction; upregulation is indicated in yellow, and downregulation in blue/green; gene names are shown on the left. F-N Combined feature plots showing expression of selected genes differentially expressed between top expanded clones and the polyclonal infiltrate. Normalized expression level for each cell is color-coded (red) and overlaid onto UMAP plots. TC: T cells; UMAP: Uniform Manifold Approximation and Projection. TCR: T-cell receptor