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. 2020 Dec 18;11:584979. doi: 10.3389/fimmu.2020.584979

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Copyright © 2020 Liang, Hu, Zhang, Lin, Zhang, Li, Zhu, Xue, Chen, Li and Wang

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Characterization of T cells during liver fibrosis. (A) tSNE clustering as in c, but colored by T cell type (CD4 T, CD8 T, γδ T, and NKT). (B) The number and percentage of T cell types. (C) Flow cytometry for CD4 T cells (CD4⁺), CD8 T cells (CD8⁺) and NKT cells (NK1.1⁺, CD3e⁺) in untreated, 8-week CCl₄-treated livers. (D) Trajectory analysis of CD4 T, CD8 T, γδ T and NKT cells. (E) Percentage of four T cell clusters inferred by Monocle’s pseudotime ordering as in d. (F) T cells identified using unsupervised clustering based on tSNE. (G) Heatmap showing the expression of immune-activated genes with Z scores standardized across each cluster, cell type and group (complete data available in Table S7). (H) Visualization of all T cell clusters using the activation component and differentiation component. Each dot represents a cell colored by cluster.