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. 2022 Aug 26;23(6):183–195. doi: 10.1038/s41435-022-00180-w

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© The Author(s) 2022

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 Experimental setup. CD4+CXCR5+PD-1+ cells were isolated from spleens of C57BL/6 mice infected with acute LCMV (n = 2) or chronic LCMV infection (n = 6). Each time point included two biological replicates. Cells were then sorted and sequenced to obtain both transcriptomes and TCR repertoires. B Uniform manifold approximation projection (UMAP) separated by experimental group. C Dottile plot depicting scaled expression of genes of interest separated by transcriptional clusters. D Representative donut plots depicting distribution of clonal expansion in each infection time point. Each section corresponds to a unique clone (defined by CDR3α-CDR3β nucleotide (nt) sequence) and the size corresponds to the fraction of cells relative to the total repertoire. Lowly-expanded clones (supported by only one unique cell) are colored in red. E UMAP displaying clonal expansion of Tfh cells after acute and chronic infection. Clones are defined by CDR3α-CDR3β nt sequence. Lowly-expanded clones are represented by only one unique cell, while highly-expanded clones are supported by more than one cell. F Heatmap depicting percentage of clones (defined by CDR3α-CDR3β nt sequence) using a particular TRAV gene (columns) in each cluster (rows).