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Fig. 2 | Acta Neuropathologica Communications

Fig. 2

From: Integration of single-nuclei RNA-sequencing, spatial transcriptomics and histochemistry defines the complex microenvironment of NF1-associated plexiform neurofibromas

Fig. 2

a Representative ST sample snapshot highlighting varying numbers of underlying cells per spot range. b Sequencing data from 8550 spots in 4 PN samples was aggregated and processed to identify 15 conserved spot clusters using Seurat with Harmony alignment, c ST spot clusters were annotated according to cell type deconvolution using Jaccard index analysis, which calculates marker gene overlap (displayed as heatmap) with our single-nuclei RNA-sequencing dataset. Additional annotations were generated from gene ontology searches as well as manual inspection of genelists. ST spot clusters were visualized at different resolutions using Clustree analysis. Abbreviations: Endo_fibr, Endoneurial fibroblasts; Epi_fibr, Epineurial fibroblasts; HB, Hemoglobin; LEC, Lymphatic endothelial cells; Mye_Sc, Myelinated Schwann cells; NM-SC_1 and 2, Non-myelinated Schwann cells 1 and 2; Peri_fibr, Perineurial fibroblast; Prolif_1 and 2, Proliferative 1 and 2; SC, Schwann cell; Vasc_endo_1 and 2; Vascular endothelial 1 and 2

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Acta Neuropathologica Communications

ISSN: 2051-5960

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