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. Author manuscript; available in PMC: 2020 Jun 26.
Published in final edited form as: Nat Med. 2019 Oct 7;25(10):1576–1588. doi: 10.1038/s41591-019-0590-4

Extended Data Fig. 3. Tissue–specific MetaClustering and canonical T cell definition by manual gating.

Extended Data Fig. 3.

(a) MetaLouvain Clustering of CD45+ cells from atherosclerotic plaque tissue from n=15 patients. (b) Average population frequency of plaque-derived MCs. (c, d) Representative Louvain clustered viSNE plot of n=4,386 cells overlaid by MC distribution (c), and selected myeloid surface marker expression in spectral colors (d). (e) Volcano plot of the difference of MC frequencies in ASYM (n=8 patients, left) and SYM (n=7 patients, right) atherosclerotic plaques. Statistical significance was determined using two-sided unpaired t-test with multiple comparisons corrected using the two-stage linear step up procedure of Benjamini, Krieger, and Yekutieli with FDR=0.5% (f-h) Manual gating analysis of the T-cell compartment from 24 patients. (f) viSNE plots of n=19,882 T cells overlaid by tissue origin (top left), CD4 and CD8 population (top right), effector status (bottom left), or classical definition (bottom right). (g,h) Scatter bar plots of manually gated cell populations from n=24 patients. Values are mean ± SD, p values were determined by two-sided Wilcoxon test.