scRNA+TCR-seq reveals the proportion and characteristics of dual TCR Treg cells in mouse lymphoid and non-lymphoid tissues
- Department of Immunology, Zunyi Medical University; Guizhou Provincial Research Center for Applied Immunomolecular Engineering; Guizhou Provincial Innovation Base for Graduate Education in Immunology; Guizhou Provincial Key Discipline of Immunology, China
Figures
Figure 1
Characterizes single Treg TCR and dual TCR Treg in the blood, kidney, liver, LPL, and pancreas of mice.
(A) Mouse source names, GEO accession number, total number of paired TCR Treg cells, and number and proportion of TCR paired types. (B) Four different TCR pairing types, VDJ gene family names and CDR3 AA sequences in single T cells. (C) Proportion of TCR pairing types per mouse. (D) Statistical analysis of dual TCR Treg cells and the relative proportion of single/dual TCR Treg cells in three TCR pairing types. (E) Comparative analysis of single/dual TCR Treg cell V gene usage variation. (F) Comparative analysis of single/dual TCR Treg cell J gene usage variation. (G) Differential analysis of single/dual TCR Treg cell diversity among tissues. (H) Differential analysis of single/dual TCR Treg cell clone expansion between tissues.
Figure 2
Characterizes single Treg TCR and dual TCR Treg in the inguinal lymph node (iLN), mesenteric lymph node (mLN), skin, spleen of mice.
(A) Tissue source names, GEO accession number, total number of paired TCR T cells, and number and proportion of TCR paired types. (B) Four different TCR pairing types, VDJ gene family names, and CDR3 AA sequences in single T cells. (C) Proportion of TCR pairing types per tissue. (D) Statistical analysis of dual TCR T cells and the relative proportion of single/dual TCR T cells in three TCR pairing types. (E) Comparative analysis of single/dual TCR T cell V gene usage variation. (F) Comparative analysis of single/dual TCR T cell J gene usage variation. (G) Differential analysis of single/dual TCR T cell diversity among tissues. (H) Differential analysis of single/dual TCR T cell clone expansion between tissues.
Figure 3
Comparative analysis of single Treg TCR and dual TCR Treg CDR3 overlap and gene mRNA expression in mice blood, kidney, liver, LPL, and pancreas.
(A) Clonal overlap analysis and Jaccard index of TRA/B chain CDR3 region in single/dual TCR Treg cells. (B) Tracking results of the first 10 high-frequency overlapping sequences in the CDR3 region of the TRA/B chain of single/dual TCR Treg cells between tissues. (C) Treg cell clustering results and proportion of Treg cells of the four TCR pairing types among tissues. (D) Characterized mRNA expression in single/dual TCR Treg cells. (E) Top 10 mRNA molecules highly expressed by dual TCR Treg cells in each tissue. (F) Top 10 mRNA molecules highly expressed by single/dual TCR Treg cells in each tissue and overall.
Figure 4
Comparative analysis of single Treg TCR and dual TCR Treg CDR3 overlap and gene mRNA expression in mice inguinal lymph node (iLN), mesenteric lymph node (mLN), skin, and spleen.
(A) Clonal overlap analysis and Jaccard index of TRA/B chain CDR3 region in single/dual TCR T cells. (B) Tracking results of the first 10 high-frequency overlapping sequences in the CDR3 region of the TRA/B chain of single/dual TCR T cells between tissues. (C) Treg cell clustering results and proportion of Treg cells of the four TCR pairing types among tissues. (D) Characterized mRNA expression in single/dual TCR Treg cells. (E) Top 10 mRNA molecules highly expressed by dual TCR Treg cells in each tissue. (F) Top 10 mRNA molecules highly expressed by single/dual TCR Treg cells in each tissue and overall.
Additional files
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
scRNA+TCR-seq reveals the proportion and characteristics of dual TCR Treg cells in mouse lymphoid and non-lymphoid tissues
eLife 14:RP105504.
https://doi.org/10.7554/eLife.105504.4
