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. 2023 Apr 21;14:2285. doi: 10.1038/s41467-023-37674-8

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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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Fig. 5 — A Expression of selected marker genes in neutrophils pre (T0) and at the end of (T1) NMP in individual patients (n = 7). The central line denotes the median. Boxes represent the interquartile range (IQR) of the data, whiskers extend to the most extreme data points within 1.5 times the IQR. Two-sided DESeq2 Wald-test on pseudo-bulk, p-values are adjusted to false-discovery rate (FDR) using independent hypothesis weighting (IHW). B UMAP of neutrophils colored by subclusters (N0, N1, N2, N3). C Expression of selected marker genes in neutrophil subclusters. D Relative composition of neutrophil subclusters pre (T0) and at the end of (T1) NMP. E Differential transcription factor activity (TF) activity per cell-type in T0 vs. T1 computed using DoRothEA. Red indicates upregulation of a TF-regulon in T1 compared to T0. p-values were determined using a two-sided t-test and adjusted for false-discovery rate (FDR). The t-statistics were computed using a multivariate linear model as implemented in decoupler-py. F Gene set over-representation analysis (ORA) of selected “Hallmark” gene sets per cell type in T0 vs. T1. A small p-value indicates that among genes in the gene set, more genes are differentially expressed than expected by chance (one-tailed Fisher’s exact test).