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. 2023 Aug 14;24(9):1565–1578. doi: 10.1038/s41590-023-01575-1

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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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Extended Data Fig. 1 — a, UMAP of blood and liver MAIT cells and conventional memory T (T_mem) cells colored by the 14 identified clusters. n = 89,456 cells from 12 donors (11 blood, 7 liver). b, UMAPs of blood and liver MAIT and T_mem cells colored by CD4 gene (left) and protein (right) expression. c,d, Bar plots showing the log₂ fold change in expression of the top ten genes upregulated in MAIT cells compared with T_mem cells, and vice versa, in the blood (c) and liver (d). e, Pearson’s correlation between the log₂ fold change in protein expression between MAIT and T_mem cells in the blood, and MAIT and T_mem cells in the liver. f,g, Bar plots showing the log₂ fold change in expression of the top ten proteins upregulated in MAIT cells compared with T_mem cells, and vice versa, in the blood (f) and liver (g). h,i, Proportion of cells in each cluster (analysis of MAIT cells from six matched blood-liver donors) from Exp 1 and Exp 2 (h) and from each donor (i). j, Expression of CD56, CD38 and CD244 (2B4) proteins in blood and liver MAIT cells. k, Flow cytometry plot showing CD69 expression on blood and liver MAIT cells from two representative donors. l, Gene set enrichment analysis of liver compared with blood T_mem cells using published human and mouse tissue-resident memory T cell gene signatures. NES, normalized enrichment score. m, Over-representation analysis on the genes significantly upregulated in liver T_mem cells compared with blood T_mem cells. Top 15 gene ontology (GO) terms and associated Benjamini–Hochberg adjusted P values are shown. n, Heatmap showing activity (row-scaled AUCell scores) of the 20 most differentially active regulons (largest difference in average AUCell score) between matched blood and liver MAIT cells in Exp 2. n = 3 donors. o-q, Over-representation analysis on predicted ATF3 (o), NFKB2 (p) and REL (q) target genes. Top ten GO terms and associated Benjamini–Hochberg adjusted P values are shown.