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. 2021 Jun 23;12:3895. doi: 10.1038/s41467-021-23995-z

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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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Fig. 4 — a Enrichment protocol for derivation of single cell suspensions from biosamples. b UMAP projection of CD45+CD34+-enriched glioblastoma cells, color coded for graph-based clusters. c Cell type annotation by SingleR in the CD34+CD45+-enriched glioblastoma sample. HSPC Hematopoietic stem and progenitor cell. d Marker expression for immune (PTPRC), HSPCs (CD34, SPINK2, GATA2), and myeloid lineages (CD14, ITGAM, TMEM119, CD33) in the glioblastoma dataset. Dashed line indicates the HSPC cluster defined in (c). e SingleR annotation of HSPC subsets in glioblastoma (GBM), tumor-free brain (TFB), bone marrow (BM), and blood samples magnetically enriched by CD34+CD45+ are shown as UMAP projections. Stacked barplot indicates fractions of HSPC subsets as annotated in the four datasets with absolute numbers shown within bars. p value determined by a two-tailed Fisher’s exact test. HSC Hematopoietic stem cell, MPP Multipotent progenitor, CMP Common myeloid progenitor, GMP Granulocyte–monocyte progenitor, CLP Common lymphoid progenitor, MEP Megakaryocyte–erythroid progenitor. f The left panel shows UMAP projection of the integrated dataset used for cell cycle and differential gene expression analysis. Cells derived from each sample are displayed by different color-coding. Right panel: singleR annotation of HSPC subsets in the integrated dataset are highlighted on the UMAP plot by the the corresponding colors shown in the legend. NK cells Natural killer cells. g UMAP plot of cycling and non-cycling cells computed by Seurat. Stacked barplots show the proportion of cycling and non-cycling HSPC subsets in the glioblastoma (GBM), bone marrow (BM), and blood sample. p value determined by a two-tailed Fisher’s exact test corrected by the Benjamini Hochberg procedure. h Heatmaps show a selection of top differentially expressed genes between bone marrow-resident and circulating HSPC subsets vs tumor-associated HSPCs as computed by MAST. The complete dataset is provided in the Supplementary Data 5–8. Source data are provided as a Source Data file.