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. 2021 Jul 20;7:52. doi: 10.1038/s41421-021-00280-3

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© The Author(s) 2021

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. 1 — a Overview of experimental design. CD3⁺ T cells from the blood of 8 PD patients and 6 healthy controls were sorted by FACS and simultaneously subject to single-cell transcriptome and immune sequencing with 5’ V(D)J capture. Single-cell TCR data from cerebrospinal fluid were downloaded from GEO with accession ID GSE134578. Batch effect correction and unsupervised clustering were performed after merging single-cell datasets. b UMAP projection of 103,365 single T cells, showing 21 clusters. Each dot corresponds to one cell and is colored according to cell cluster. c Dot plot shows the expression of marker genes for 21 cell clusters. The size of the dot corresponds to the percentage of cells expressing the gene in each cluster, and the color represents the average log normalized gene expression. Markers were ordered to visualize the differences between cell types. d UMAP projection of T cells colored by the 5 major T cell types, including CD8⁺ T cells (CD8), CD4⁺ T cells (CD4), mucosal-associated invariant T cells (MAIT), gamma delta T cells (gdT) and double-negative T cells (DNT). e Pie charts showing the percentages of the five major T cell types in the blood of PD patients and healthy controls. For each cell type, the percentage was obtained by dividing the number of cells in that cell type by the total number of cells in all PD patients or in all healthy controls. f Barplot showing the percentages for different T cell types identified from single cell analysis. Error bars represent standard error of the mean.