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. 2021 Nov 22;22(12):1577–1589. doi: 10.1038/s41590-021-01059-0

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© The Author(s) 2021

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. 5 — Related to Fig. 2. a. Heatmap investigating if the fraction of variance explained by the different covariates is correlated to antigen-level technical covariates. P values were calculated from Pearson correlation using a one-sided test based on the t-distribution. b-d. Dot plot depicting the expression of the 10–20 surface markers with the highest fraction of variance explained by B cell subtype (b), myeloid subtype (c) and NK cell subtype (d). Color indicates mean normalized expression, point size indicates the fraction of cells positive for the marker. Automatic thresholding was used to identify positive cells, see Methods, section ‘Thresholding of surface marker expression’ for details. e. UMAPs highlighting the scores for various biological processes, as computed using the gene lists from Supplementary Table 7. f. Bar charts depicting the markers with the highest fraction of variance explained by cytotoxicity score (pink), stemness score (red) and S-phase score (dark red), and the corresponding model coefficients. See Supplementary Table 7 for the gene lists used for calculating these scores. g. Pseudotime of all 97 surface proteins for the five trajectories (B cells, cDCs, Monocytes, Late erythroid progenitor and Megakaryocyte progenitor). Markers were clustered according to their expression pattern using tradeseq (van den Berge, 2020). The density plots indicate the differentiation stages along the pseudotime.