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. 2023 Jul 6;5(7):1188–1203. doi: 10.1038/s42255-023-00834-7

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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. 3 — a, Dot plot of gene expression (log₂ RPKM) of macrophage and dendritic cell markers. Colour intensity indicates expression level and dot size indicates gene expression frequency (percentage of cells expressing the gene). b, Heatmap of gene expression (log₂ RPKM) of macrophage markers in the LM2 and cDC2 subclusters. c, Dot plot of gene expression of macrophage and cDC2 marker in our human myeloid cell data and d, in a published data set (GSE192742) of human myeloid cells by Guilliams et al. e, Radar plot visualization of the assigned cell-type score by the neural network classifier for each individual cell in the LM2/cDC2 subclusters and control cells; colours indicate cell cluster. f, Accuracy of the neural-network classifier in learning 261 single cells of LM2, cDC2 and the control cell types (LM1, LM3 and LM4) visualized as a learning curve. g, Subcluster analysis of cDC2 cells from the published data set of human myeloid cells by Guilliams et al. and h, dot plot of macrophage and cDC2 markers for each subcluster. i, UMAP visualisation of the cDC2 subclusters from g in relation to other myeloid populations. Orange rectangle indicates position of cluster cDC2-4. j, Integration of the human NPC data with a published data set (E-MTAB-7407) of human embryonic liver cells by Popescu et al. k, Dot plot of gene expression of previously published evolutionary conserved marker genes of Kupffer cells in mice and humans by Guilliams et al. l, Dot plot of gene expression (log₂ RPKM) of monocyte markers. Data are presented as mean ± s.e.m. P values were calculated by two-way ANOVA with adjustment for multiple comparisons. RPKM, Reads per kilobase of exon model per million mapped reads; pDC, plasmacytoid dendritic cells; cDC1, type 1 dendritic cells; cDC2, type 2 dendritic cells; KC, Kupffer cells; moKCs, monocyte-derived KCs; LAMs, lipid-associated macrophages; HSC/MPP, hematopoietic stem cells and multipotent progenitors; early L/TL, early lymphoid/T lymphocyte.