biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsJakob NücklesIllumina iScan SystemIllumina Hybridization OvenThermal cycler, Eppendorf ThermoMixer CLeica microtome, 1 mm biopsy punchPromega Maxwell RSC instrumentmethylation profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16255DNA methylation profiling of glioblastoma, IDH-wildtype (GBM, IDH wt) to explore biomarkers linked to clinical outcome under Tumor Treating Fields (TTFields). FFPE tumor tissue was pathology-reviewed and macro-dissected; DNA was bisulfite-converted and hybridized to Illumina Infinium MethylationEPIC BeadChips (v1.0 and v2.0). The submission provides raw IDATs. Methylation classes and copy-number profiles were derived and integrated with clinical covariates to test whether (epi-) genetic features stratify prognosis and can guide TTFields initiation.biostudies-arrayexpressScaning - After staining and final washes, dried BeadChips were scanned on an Illumina iScan System using the Infinium MethylationEPIC application file and default settings according to the manufacturer’s instructions. Images for red and green channels were acquired and feature extraction was performed by iScan Control Software. Raw intensity signals were written as paired IDAT files (one Red and one Green per array). No background correction or normalization was applied at extraction; IDAT files were used for downstream QC and processing.Sample Collection - Formalin-fixed paraffin-embedded (FFPE) brain tumor tissue was reviewed on H and E sections by a board-certified neuropathologist. Regions with ~80% tumor cell content (or the highest available in recurrent cases) were macrodissected. Tissue was excised from marked areas using a 1 mm punch (depth <= 3 mm) and transferred for nucleic acid extraction.Labeling - For Illumina Infinium HD methylation assay, bisulfite-converted DNA underwent whole-genome amplification, enzymatic fragmentation, and single-color biotin labeling according to the manufacturer’s protocol. Detection used streptavidin-Cy3 staining. This is a single-color assay; no dye-swap was used.Hybridization - Bisulfite-converted (and for FFPE, restored) DNA was denatured and hybridized to Illumina Infinium MethylationEPIC BeadChips (v1.0 and v2.0) per manufacturer’s instructions. After overnight hybridization, single-base extension and staining were performed on the BeadChips. Arrays were scanned on an Illumina iScan, and IDAT files were generated for downstream processing.Nucleic Acid Extraction - After deparaffinization, DNA were extracted from FFPE tissue using the Promega RSC FFPE Plus DNA/RNA kits on a Maxwell instrument, following the manufacturer’s instructions. Elution volume was 40 uL nuclease-free water. DNA concentration was measured with Quantus Fluorometer.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsJakob NücklesfalsePTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patientsDNA methylation profiling of glioblastoma, IDH-wildtype (GBM, IDH wt) to explore biomarkers linked to clinical outcome under Tumor Treating Fields (TTFields). FFPE tumor tissue was pathology-reviewed and macro-dissected; DNA was bisulfite-converted and hybridized to Illumina Infinium MethylationEPIC BeadChips (v1.0 and v2.0). The submission provides raw IDATs. Methylation classes and copy-number profiles were derived and integrated with clinical covariates to test whether (epi-) genetic features stratify prognosis and can guide TTFields initiation.2025-12-04T00:00:00Z2026-05-27T13:00:42.954Z2025-11-21T14:57:29.119ZE-MTAB-16255EFO_0002944EFO_0003814EFO_0003813EFO_0002759EFO_0005518EFO_0003815