Fig. 1: Overview of workflow and sample information. | Nature Communications

Fig. 1: Overview of workflow and sample information.

From: Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas

Fig. 1

a Illustration of the overall workflow. Examples images for SpotClean-adjusted gene expression (OLIG2) and BANKSY-based spatial clustering for DMG1 are shown. b UMAP of all Harmony-integrated spatial transcriptomic spots (n = 26, 460) from all samples (n = 11). Colors represent different samples. Clusters of peritumor spots are highlighted by blue dashed lines. c Overview of the workflow for CNV-based estimation of tumor cell content. GBM4 is shown as an example. Colors indicate the predicted tumor cell content score. d UMAP of all Harmony-integrated spatial transcriptomic spots from all samples (n = 26,460 spots). Colors indicate the predicted tumor cell content score. The same clusters of peritumor spots in b are highlighted by blue dashed lines. e The colocalization of CNV and H3K27M mutation in spots from DMG samples (n = 5). The number of spots from each sample is indicated.

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