Single cell RNA and ATAC sequencing data from GBM patients

Glioblastoma cells infiltrate and incorporate into the normal brain parenchyma. We conduct unbiased multimodal single-cell and spatial sequencing to capture GBM cells and the surrounding tumor microenvironment using a regional sampling strategy. For each patient, we profile the peritumoral region, tumor edge, and tumor core, providing a comprehensive characterization of the transcriptional and epigenetic landscape of GBM spatial heterogeneity, with a specific focus on infiltrative cells.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets

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Dataset ID	Description	Technology	Samples
EGAD50000000778	This dataset contains snRNA-seq data of 11 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei were dissociated from frozen tissue using Chromium Nuclei Isolation Kit. Nuclei barcoding, cDNA preparation, and library construction were performed following the Evercode WT or WT mini User Manual, by combinatorial barcoding to assign a unique barcode to each cell.	Illumina NovaSeq 6000	11
EGAD50000001837	This dataset contains snRNA-seq data of 5 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei dissociation was performed following the nuclei isolation for single-cell ATAC-seq (10x Genomics; CG000169) with matched peri-tumoral and tumor core samples. Subsequent single-cell methylation sample preparation followed Scale Biosciences single-cell methylation kit protocol v1.0. mplification adaptors through ligation and adding a second barcode though indexed PCR reaction following Scale Biosciences single-cell methylation kit protocol v1.0. We employed the TWIST human methylome panel for targeted enrichment of informative methylation sites.	Illumina NovaSeq X	5
EGAD50000001838	This dataset contains snRNA-seq data of 26 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit, nuclei were barcoded and RNA and ATAC libraries were constructed, allowing for simultaneous capture of transcriptome and epigenome from the same cells.	Illumina NovaSeq X	26