{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Hendrikus Ariese"],"instrument_platform":["Sony SH8000S Cell Sorter","Illumina iScan"],"study_type":["methylation profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15559"],"description":["Diffuse midline glioma (DMG) is a lethal pediatric brain cancer with limited treatment options. We developed a human brainstem organoid model to study H3.3K27M-driven DMG, enabling formation of patient-like tumors with molecular heterogeneity. To characterize the resulting tumor we performed DNA methylation and compared the generated tumor with methylation data from DMG, pGBM and PFA ependymoma patients."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 3 Tumor-bearing brain organoids (DMGO) from the same batch and age were pooled. For timepoints after Matrigel embedding, Cell Recovery Solution (Corning, 354253) was used to dissolve the Matrigel. Organoids were incubated in this solution at 4°C for 15 minutes, halved, and washed in HBSS without Ca²⁺ and Mg²⁺. A single cell supsension was obtained using the Neural Tissue Dissociation Kit (Miltenyi Biotec, 130-092-628) according manufactures protocol. Single cells were washed with PBS 10%FBS and sorted for GFP using the Sony SH800S Cell Sorter. GFP positive cells were washed with PBS 10%FBS and snapfrozen for later processing.","Nucleic Acid Extraction - DNA was isolated using the Qiagen DNAeasy Blood & Tissue kit according manufactures protocol.","Labeling - Nucleic acid labelling was done using the Illumina MethylationEPIC v2.0 kit according manufactures protocol.","Hybridization - Hybridization was done using the Illumina MethylationEPIC v2.0 kit according manufactures protocol.","Scaning - Array scanning was done using the Illumina MethylationEPIC v2.0 kit according manufactures protocol."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Hendrikus Ariese","Anne Rios"],"additional_accession":[]},"is_claimable":false,"name":"Methylation profiling of DMGO","description":"Diffuse midline glioma (DMG) is a lethal pediatric brain cancer with limited treatment options. We developed a human brainstem organoid model to study H3.3K27M-driven DMG, enabling formation of patient-like tumors with molecular heterogeneity. To characterize the resulting tumor we performed DNA methylation and compared the generated tumor with methylation data from DMG, pGBM and PFA ependymoma patients.","dates":{"release":"2025-09-20T00:00:00Z","modification":"2025-09-20T01:03:44.821Z","creation":"2025-09-08T10:45:43.914Z"},"accession":"E-MTAB-15559","cross_references":{"Biostudies":["E-MTAB-15147"],"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0002759","EFO_0005518","EFO_0003815"]}}