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. 2023 Sep 28;14:6062. doi: 10.1038/s41467-023-41691-y

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — (Related to Supplementary Fig. 3). FACS analysis and gating strategies for sorting of endothelial and stromal cells in the central bone marrow (CBM; a) and bone lining (BL; b) cell compartments of mice 1 day post platelet depletion (GPIbα antibody treatment). Control mice received isotype (IgG) control antibody. Bar diagrams represent mean ± SD frequencies (%) of each cell population among total non-hematopoietic CD45^–Ter119^– cells. Data are from 3 mice per group in 3 (a) and 2 (b) independent experiments. *p < 0.05; ns non-significant (p > 0.05); assessed by two-sided t-test. c–g RNA-sequencing analysis of the endothelial/stromal cell compartments of mice 1 day post platelet depletion. c Expression (FPKM) of genes characterizing the different niche cell populations. d Principal component analysis of normalized gene expression of the different cell populations investigated. e Number of differentially expressed (DE) genes between IgG and GPIbα treated mice (adjusted p value (q)<0.05), in each niche cell population investigated. f Volcano plots and g gene ontology (GO) terms analysis of genes differentially expressed in CBM endothelial cells (EC) and Lepr⁺ perivascular (PV) cells. In f, red dots indicate significantly DE genes (q < 0.05. For all panels data represent mean ± SD FPKM of 3 biological replicates from 2 independent experiments. OB osteoblasts, OBP osteoblast progenitors, PαS Pdfgrα⁺Sca1⁺ mesenchymal progenitors. See also Supplementary Fig. 3.