Single cell RNA-sequencing of GSCs and GBM tumours - EGA European Genome-Phenome Archive

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006802	Single nuclei RNA-sequencing of snap frozen glioblastoma tumor tissue with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome with intron using CellRanger.	Illumina HiSeq 2500	10
EGAD00001006803	Single cell RNA-sequencing of fresh glioblastoma tumor biopsies with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.	Illumina HiSeq 2500	23
EGAD00001006804	Single cell RNA-sequencing of glioblastoma stem cell (GSC) lines with 10x Genomics 3' expression (v2 chemistry). Aligned to GRCh38 reference genome using CellRanger.	Illumina HiSeq 2500	29

Publications	Citations
A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours. Hamed AA, Kunz DJ, El-Hamamy I, Trinh QM, Subedar OD, Richards LM, Foltz W, Bullivant G, Ware M, Vladoiu MC, Zhang J, Raj AM, Pugh TJ, Taylor MD, Teichmann SA, Stein LD, Simons BD, Dirks PB. Nat Commun 13: 2022 4178	23
Glioblastoma heterogeneity at single cell resolution. Eisenbarth D, Wang YA. Oncogene 42: 2023 2155-2165	97
Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence. Andrieux G, Das T, Griffin M, Straehle J, Paine SML, Beck J, Boerries M, Heiland DH, Smith SJ, Rahman R, Chakraborty S. Genome Med 15: 2023 48	22
Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets. Vinel C, Boot J, Jin W, Pomella N, Hadaway A, Mein C, Zabet NR, Marino S. BMC Biol 23: 2025 26	4
Large-scale bulk and single-cell RNA sequencing combined with machine learning reveals glioblastoma-associated neutrophil heterogeneity and establishes a VEGFA<sup>+</sup> neutrophil prognostic model. Yang Y, Liu Z, Wang Z, Fu X, Li Z, Li J, Xu Z, Cen B. Biol Direct 20: 2025 45	4
Charting the Single-Cell and Spatial Landscape of IDH-Wildtype Glioblastoma with GBmap. Ruiz-Moreno C, Salas SM, Samuelsson E, Minaeva M, Ibarra I, Grillo M, Brandner S, Roy A, Forsberg-Nilsson K, Kranendonk MEG, Theis FJ, Nilsson M, Stunnenberg HG. Neuro Oncol 27: 2025 2281-2295	7
Integrating Machine Learning and Multi-Omics to Explore Neutrophil Heterogeneity. Lin Z, Yang T, Chen D, Zhang P, Luo J, Chen S, Gu S, Shen Y, Tang T, Chang T, Dong L, Zhang C, Tang Z. Biomedicines 13: 2025 2171	0
Machine learning-enhanced discovery of a basement membrane-related gene signature in glioblastoma via single-cell and Spatial transcriptomics. Liu Z, Yang Y, Fang H, Han M, Qi P, Fan Y, Li J, He S, Wang L. J Transl Med 23: 2025 1325	0