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. 2022 May 26;54(6):817–826. doi: 10.1038/s41588-022-01066-3

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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. 2 — a, Number of significant eGenes detected at each activation time point. Colors represent cell types (blue, T_N; red, T_M). b, Number of significant eGenes shared between cells sampled at each time point. c, Example of T memory cell-specific eQTLs detected at 16 h and 40 h. Box plots show mean expression value of the gene in each sample (Z-scored), stratified by genotype at the genomic position of the lead eQTL variant (X axis). Each dot represents a measurement from a separate individual. Central lines indicate the median, with boxes extending from the 25th to the 75th percentiles. Whiskers further extend by ±1.5 times the interquartile range from the limits of each box. N of biologically independent samples: T_N NME4: 99, T_M NME4: 96, T_N P2RX4: 89, T_M P2RX4: 89. P values were derived using tensorQTL and corrected as described in Methods. d, Pairwise comparison of eGenes shared between cell subpopulation. Only subpopulations with >100 eGenes were analyzed. e, Scatter plot showing the correlation between number of cells per donor and number of detected eGenes in each cluster. f, Subpopulation-specific eQTLs detected in IFN-responsive clusters. Bar plot (top) indicates the number of eGenes detected in the IFN-responsive subpopulation that are shared with naive T cells as a whole. Boxplots (bottom) show an example eQTL specific to this subpopulation. Each dot represents a measurement from a separate individual. Central lines indicate the median, with boxes extending from the 25th to the 75th percentiles. Whiskers further extend by ±1.5 times the interquartile range from the limits of each box. N of biologically independent samples: T_N IFN FBXL18: 96, T_N FBXL18: 87, P values were derived using tensorQTL and corrected as described in Methods. g, Number of subpopulation-specific eQTLs detected in T_CM and T_EM cells. Bar plots (top) indicate numbers of eGenes detected in T_CM and T_EM subpopulations that are shared with memory T cells as a whole. Boxplots (bottom) show an example eQTL specific to the T_CM subpopulation. Each dot represents a measurement obtained from a separate individual. Central lines indicate the median, with boxes extending from the 25th to the 75th percentiles. Whiskers further extend by ±1.5 times the interquartile range from the limits of each box. N of biologically independent samples: T_CM GNPDA1: 100, T_EM GNPDA1: 103, T_M GNPDA1: 97. P values were derived using tensorQTL and corrected as described in Methods. ER, endoplasmic reticulum; nTreg, natural regulatory T cells.