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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. 5 — a Left, Uniform manifold approximation and projection (UMAP) displaying two independent scRNA-seq data sets from C57BL/6 and two independent Hivep3^−/− thymic iNKT cells colored by sample of origin after MNN batch-correction. Right, UMAP colored by inferred cluster identity for the integrated dataset. b Individual UMAP plots for each biological sample in the dataset, with the sample and number of cells passing quality control and filtering indicated above each plot. c Cell cycle scores were computed for each cell in the dataset using the R Seurat package and then categorized into S, G2 or G1/G0 phases. Pie charts depict the proportion of C57BL/6 (Left) and Hivep3^−/− (Right) cells within each cluster belonging to a given phase of the cell cycle. d Heatmap displaying expression levels of 65 differentially expressed genes across stage 0 iNKT cells in the dataset. The sample to which a given cell belongs are indicated at the top of the heatmap. e, f Violin plots displaying aggregate expression levels per sample of genes that are expressed higher in C57BL/6 (e) or higher in Hivep3^−/− (f) stage 0 iNKT cells.