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. 2023 Sep 21;24(10):1725–1734. doi: 10.1038/s41590-023-01608-9

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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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Fig. 1 — a, Overview of study design, in which PBMCs were collected from six healthy donors at day 0, day 2, day 10 and day 28 during the BNT162b2 mRNA vaccination process and comprehensive analyses using both CITE-seq and ASAP-seq were performed on these samples. b, Uniform manifold approximation and projection (UMAP) visualizations of 113,897 single cells obtained as in a profiled with CITE-seq and clustered by a weighted combination of RNA and protein modalities. Cells are colored based on level-2 annotation (level-1 and level-3 annotations; Extended Data Fig. 2a). c, Single-cell heatmap showing activation of interferon response module within CD14⁺ monocytes. d, Milo analysis of differentially abundant cell states between day 0 and day 28 samples as in panel a. UMAP on the left is color coded by timepoint. Right plot indicates embedding of the Milo differential abundance. Each node represents a neighborhood, node size is proportional to the number of cells, and neighborhoods are colored by the level of differential abundance. Nhood, neighborhood. e, Beeswarm plot showing the log-fold distribution of cell abundance changes between day 0 and day 28 samples as in a. Neighborhoods overlapping the same cell population are grouped together, neighborhoods exhibiting differential abundance are colored in red. f, Violin plots with protein upregulation of CD38, HLA-DR and CD278 (ICOS) in VI-A and VI-B CD8⁺ T cells compared with CD8⁺ naive, CD8⁺ T_CM and CD8⁺ T_EM cells. g, Heatmap showing mRNA expression of 50 marker genes for VI-A CD8⁺ T cells, as well as cell-cycling genes highly expressed in VI-B CD8⁺ T cells. For visualization purposes, a randomly selected subset of CD8⁺ T_EM cells are presented. HSPC, hematopoietic stem and progenitor cell; NK, natural killer; pDC, plasma dendritic cell; T_CM, central memory T cell; T_EM, effector memory T cell. ASDC, AXL⁺ dendritic cell; CTL, cytotoxic T cell; dnT, double-negative T cell; gdT, gamma-delta T cell; MAIT, mucosal associated invariant T.