Spatial Transcriptome data
Spatial transcriptomics experiments were performed using the 10X Visium Spatial Gene Expression kit, following manufacturer's instructions. The data was generated using 13 GBM, 2 IDHmut G3 astrocytoma, 1 IDHmut G4 astrocytoma, and 1 normal brain sample.
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scRNA-Seq data
Single-cell RNA-Seq was generated for 2 IDHmut G3 astrocytoma, 2 IDHmut G4 astrocytoma, 1 IDHwt G3 astrocytoma, 1 IDHmut G3 oligodendroglioma, 26 glioblastoma, 3 normal brain, and 3 other samples. The grade 4 samples were prepared from both the core and the periphery of the tumor.
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Cite-Seq data
Cite-Seq RNA-Seq was generated for 11 glioblastoma, and 1 normal brain samples. The grade 4 samples were prepared from both the core and the periphery of the tumor.
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Reference dataset
The following datasets were used to build the reference single-cell dataset:
1. Allen institute: single-nucleus transcriptomes from 76,533 total nuclei derived from 2 post-mortem human brain specimens, to survey cell type diversity in the primary motor cortex (M1C or M1) (Sunkin et al., 2013). We used the original publication cell type annotation for the dataset.
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2. Xie et al.: single-cell data generated from tumor core and paired surrounding
peripheral tissue in 4 glioblastoma patients (Xie et al., 2021). Specifically, for endothelial cells. RCC was performed to find clusters and cell types were
identified using scMAGIC (Zhang et al., 2022).
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3. Winkler et al: single-cell data generated using dissociated vascular cells isolated from the adult human brain and arteriovenous malformations (Winkler et al., 2022). We used the original publication cell type annotation for the dataset.
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4. Abdelfattah et al.: single-cell data generated from 44 GBM (new diagnosed +
recurrent) and LGG samples (Abdelfattah et al., 2022). RCC was performed to
find clusters and cell types were identified using scMAGIC.
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5. TAM-citeseq: CITE-seq data of myeloid cells from newly diagnosed and
recurrent GBM samples (Pombo Antunes et al., 2021). We used the original
publication celltype-annotation for the dataset.
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6. Matthewson et al.: single-cell data of glioma-infiltrating T cells isolated from fresh tumor samples in 31 adult patients with either IDH-wildtype glioblastoma (GBM) or IDH-mutant glioma (IDH-G) (Mathewson et al., 2021). We used the original publication cell type annotation for the dataset.
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Bulk RNA-Seq data
RNA-Seq data was generated for 84 glioblastoma samples.
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Supplementary files
supplementary Tables
supplementary File 1
supplementary File 2