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. 2022 Nov 9;13(2):364–385. doi: 10.1158/2159-8290.CD-22-0199

Figure 3.

Figure 3. scRNA-seq confirmed that hematopoietic and stromal cell lineages within organoids showed transcriptional similarity to human hematopoietic tissues. A, Uniform manifold approximation and projection (UMAP) plot showing annotated cell clusters. B, Gene set enrichment analysis of differentially expressed genes for each cluster using a curated set of 64 hematopoietic lineage gene sets. DC, dendritic cell; GMP, granulocyte-macrophage progenitor; HSC, hematopoietic stem cell; KEGG, Kyoto Encyclopedia of Genes and Genomes; LMPP, lymphoid-primed multipotent progenitor; MEMP, megakaryocyte-erythroid-mast cell progenitor; MK, megakaryocyte; MkE, megakaryocyte-erythroid; MPP, multipotent progenitor; NK, natural killer cell; pDC, plasmacytoid DC; prog., progenitor; VCAM EI, VCAM erythroblastic island; WP, WikiPathways. C, Expression of canonical stromal and hematopoietic cell genes for each of the annotated clusters. The color scale represents the average level of expression, and the circle size shows the percentage of cells within each cluster in which expression was detected for each gene. D and E, FDG showing differentiation trajectories for hematopoietic (D) and stromal (E) compartments, superimposed with expression scores of lineage signature gene sets. F, Organoid cells projected onto a published dataset of human hematopoietic and stromal cells using the Symphony package (33). Mono-Mac, monocyte-macrophage. See also Supplementary Figs. 2 and 3 and Supplementary Tables S1 and S2.

scRNA-seq confirmed that hematopoietic and stromal cell lineages within organoids showed transcriptional similarity to human hematopoietic tissues. A, Uniform manifold approximation and projection (UMAP) plot showing annotated cell clusters. B, Gene set enrichment analysis of differentially expressed genes for each cluster using a curated set of 64 hematopoietic lineage gene sets. DC, dendritic cell; GMP, granulocyte-macrophage progenitor; HSC, hematopoietic stem cell; KEGG, Kyoto Encyclopedia of Genes and Genomes; LMPP, lymphoid-primed multipotent progenitor; MEMP, megakaryocyte-erythroid-mast cell progenitor; MK, megakaryocyte; MkE, megakaryocyte-erythroid; MPP, multipotent progenitor; NK, natural killer cell; pDC, plasmacytoid DC; prog., progenitor; VCAM EI, VCAM erythroblastic island; WP, WikiPathways. C, Expression of canonical stromal and hematopoietic cell genes for each of the annotated clusters. The color scale represents the average level of expression, and the circle size shows the percentage of cells within each cluster in which expression was detected for each gene. D and E, FDG showing differentiation trajectories for hematopoietic (D) and stromal (E) compartments, superimposed with expression scores of lineage signature gene sets. F, Organoid cells projected onto a published dataset of human hematopoietic and stromal cells using the Symphony package (33). Mono-Mac, monocyte-macrophage. See also Supplementary Figs. 2 and 3 and Supplementary Tables S1 and S2.