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. 2020 Dec 7;11:6238. doi: 10.1038/s41467-020-20073-8

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© The Author(s) 2020

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. 1 — a Uniform manifold approximation and projection (UMAP) of two independent scRNA-seq data sets from C57BL/6 thymic iNKT cells integrated using FastMNN and colored by sample of origin. b UMAP of 10,506 iNKT cells colored by inferred cluster identity. c Violin plot depicting the number of gene, number of UMI and percentage of mitochondrial genes expressed in each cluster. d Dot plot showing scaled expression of selected signature genes for each cluster colored by average expression of each gene in each cluster scaled across all clusters. Dot size represents the percentage of cells in each cluster with more than one read of the corresponding gene. e Heatmap showing row-scaled expression of the 5 highest differentially expressed genes (DEGs, Bonferroni-corrected P-values <0.05, Wilcoxson-test) per cluster for all iNKT cells. f Expression of five typical genes used to define most common iNKT cell subsets and cycling cells.