{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mario Fernandez Fraga"],"study_type":["methylation profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15178"],"description":["Pheochromocytomas and paragangliomas (PPGLs) arising in patients with SDHB mutations have a well-established predisposition to develop metastatic disease, but the molecular mechanisms underlying this aggressive behavior remain incompletely understood. We investigated how metastasis and SDHB mutation status contribute to the epigenetic landscape of PPGLs, aiming to disentangle their individual and combined effects on tumor progression. This dataset contains the DNA methylation data of the 34 PPGLs analysed in this study."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Tumor tissue samples were collected from 34 patients diagnosed with PPGL between 2003 and 2019. Patients were treated at the Hospital Universitario Central de Asturias (Spain), Mayo Clinic (USA), Hospital Universitario de Bellvitge (Spain), Hospital Provincial de Castellón (Spain), Hospital Universitario La Fe (Spain), and Complejo Universitario de Navarra (Spain). Informed consent was obtained from each patient, and the study was approved by the ethical committee of the Hospital Universitario Central de Asturias. The methods were carried out in accordance with the approved guidelines and the principles expressed in the 1975 Declaration of Helsinki, as revised in 1983.","Hybridization - DNA samples were hybridized to the Illumina HumanMethylationEPIC BeadChip array platform following the Illumina Infinium HD methylation protocol.","Nucleic Acid Extraction - Genomic DNA from paraffin-embedded (FFPE) samples was extracted with the E.Z.N.A. FFPE DNA kit (Omega Bio-Tek). Quality check was performed in 2 ng of DNA using the Infinium HD FFPE QC Assay Kit (Illumina San Diego, CA, USA). Samples with a ΔCq greater than 5 were excluded. Suitable samples were bisulfite-converted using the EZ-96 DNA Methylation-Gold™ Kit (ZymoResearch, Irvine, CA, USA), starting with 300 ng of DNA and eluting the samples in 10 μl of the elution buffer supplied by the kit (M-Elution buffer). For DNA restoration, 8 µl of the bisulfite-converted samples were used, and the Infinium HD FFPE DNA Restore Kit (Illumina) was employed. Finally, the ZR-96 DNA Clean and Concentrator-5 Kit (Zymo Research) was used to clean the DNA samples, eluting them in a final volume of 10 μl of ddH2O. DNA from frozen tissue samples was extracted using the QIAamp DNA Kit (QIAGEN, Hilden, Germany) and the EZ-96 DNA Methylation Kit (Zymo Research) was used to perform bisulfite conversion on the extracted DNA.","Labeling - Labeling was performed automatically during the post-amplification xStain process and is achieved using Biotin and DNP labelled antibodies.","Scaning - The arrays were scanned with iScan (Illumina) in accordance with the manufacturer's protocol."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Mario Fernandez Fraga","María-Dolores Chiara","Juan Ramon Tejedor"],"data_protocol":["Data Transformation - First, the minfi package (v.1.32.0) 21 was used to import fluorescence signal intensity files (IDAT) associated with each sample. The getSex function from the same package enabled tracking of self-reported sex based on probes targeting the X and Y chromosomes. Sample mislabeling was further assessed using SNP probe methylation patterns via the getSnpBeta function from minfi. After quality control evaluations, intensity values were background-corrected in minfi using the ssNoob approach 22 and subsequently, associated β-values were normalized in ChAMP (v.2.16.2) using the BMIQ method 23. All samples were finally tested to follow a bimodal-shaped beta distribution profile.  Probe filtering was performed according to the following criteria: (a) detection p-value  > 0.01 in any sample; (b) sex chromosome location; (c) cross-reactive or multi-mapping described activity [reference] and (d) presence of SNPs with MAF ≥ 0.01 at their CpG or SBE sites (dbSNP v.147). The final number of probes that passed through all the filters was 754,581. All data analyses were performed using the statistical software R (v.4.0.2)."],"additional_accession":[]},"is_claimable":false,"name":"Epigenetic and metabolic rewiring in metastatic pheochromocytomas and paragangliomas driven by SDHB mutations (DNA methylation data)","description":"Pheochromocytomas and paragangliomas (PPGLs) arising in patients with SDHB mutations have a well-established predisposition to develop metastatic disease, but the molecular mechanisms underlying this aggressive behavior remain incompletely understood. We investigated how metastasis and SDHB mutation status contribute to the epigenetic landscape of PPGLs, aiming to disentangle their individual and combined effects on tumor progression. This dataset contains the DNA methylation data of the 34 PPGLs analysed in this study.","dates":{"release":"2025-12-23T00:00:00Z","modification":"2025-12-23T11:50:35.864Z","creation":"2025-05-29T09:36:49.213Z"},"accession":"E-MTAB-15178","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0002759","EFO_0005518","EFO_0003816","EFO_0003815"]}}