Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

ABSTRACT: DNA 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.

INSTRUMENT(S): Illumina iScan System, Illumina Hybridization Oven, Thermal cycler, Eppendorf ThermoMixer C, Leica microtome, 1 mm biopsy punch, Promega Maxwell RSC instrument

ORGANISM(S): Homo sapiens

SUBMITTER: Jakob Nückles

PROVIDER: E-MTAB-16255 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Placental methylation profile in women exposed to fluoride and its association with kidney volume at birth

Project description:This experiment investigates the relationship between maternal fluoride exposure during pregnancy and DNA methylation patterns in the placenta, aiming to identify epigenetic alterations associated with reduced kidney volume at birth. Placental samples were collected from term deliveries and classified according to maternal fluoride concentration and neonatal kidney volume. Genomic DNA was extracted, bisulfite-converted, and hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip to quantify methylation across more than 935,000 CpG sites. Data preprocessing, quality control, and normalization were performed using the SeSAMe package in R, following Illumina’s recommended pipeline for EPIC v2.0 arrays. Differentially methylated positions and regions were identified to explore potential epigenetic mechanisms linking prenatal fluoride exposure with altered renal development.

2026-04-07 | E-MTAB-16226 | biostudies-arrayexpress

DNA methylation profiling of pediatric central nervous system tumors in a Brazilian public healthcare setting

Project description:This study aimed to validate the use of DNA methylation profiling in the classification of pediatric central nervous system (CNS) tumors within the Brazilian public healthcare system. A total of 16 tumor samples from pediatric patients previously diagnosed with medulloblastoma or ependymoma—the two most common CNS tumors in children—were analyzed. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue and processed using the Infinium MethylationEPIC BeadChip array (Illumina). Methylation data were interpreted using two versions of the DKFZ brain tumor classifier (v11b4 and v12.5) and compared to reference diagnoses established through routine histopathological and molecular analyses. The study was conducted at the largest public hospital complex in Latin America and reflects practical challenges and opportunities for implementing precision diagnostics in real-world, resource-limited healthcare settings.

2026-03-31 | E-MTAB-15074 | biostudies-arrayexpress

Genotyping by array of 297 adult-type diffuse gliomas comprise IDH-mutant astrocytomas, IDH-mutant 1p/19q codeleted oligodendrogliomas, and IDH-wildtype glioblastomas

Project description:Adult-type diffuse gliomas comprise IDH-mutant astrocytomas, IDH-mutant 1p/19q codeleted oligodendrogliomas (ODG), and IDH-wildtype glioblastomas (GBM). GBM display genome instability, which may result from two genetic events leading to massive chromosome alterations: chromothripsis (CT) and whole-genome duplication (WGD). The better prognosis of the latter may be related to their genome stability compared to GBM. Pangenomic profiles of 297 adult diffuse gliomas were analyzed at initial diagnosis using SNP arrays, including 192 GBM and 105 IDH-mutant gliomas (61 astrocytomas and 44 ODG). Tumor ploidy was assessed with Genome Alteration Print and CT events with CTLPScanner and through manual screening.

2024-12-24 | E-MTAB-13542 | biostudies-arrayexpress

DNA Methylation of gDNA from blood and bronchoalveolar lavage of tuburbulosis patients with and without type 2 diabetes via Illumina Infinium MethylationEPIC array

Project description:Tuberculosis (TB) remains a leading cause of illness and death globally. Type 2 diabetes (T2D) patients are more likely to become infected with Mycobacterium tuberculosis (M.tb). When they are infected, they are more likely to develop active TB disease and to present with more severe TB and those who receive TB treatment are more likely to experience adverse treatment outcomes. Genomic DNA (gDNA) was isolated from unstimulated whole blood and bronchoalveolar lavage (BAL) cells. Analysis of methylation arrays was carried out following the Bioconductor ‘methylationArrayAnalysis’ workflow, using the IlluminaHumanMethylationEPICanno.ilm10b4.hg19 annotation set for Illumina MethylationEPIC arrays. Probes were excluded where detection p-value was <0.01, where they were located on the Y chromosome, or were annotated as containing SNPs or known to be cross-reacting. Probes on the X chromosome were retained as only females were included in this analysis. Background correction was carried out via the normal-exponential out-of-band (Noob) method and probe intensities were quantile normalized. To identify differentially methylated positions (DMPs), the data was filtered using the criteria shown in extended data figure 8. To permit comparison between DMPs a secondary cutoff of uncorrected p<0.01 and beta values >0.8 and <0.2 was retained. Gene set enrichment testing was carried out via the “gsameth” function in the missMethyl package using hallmark and GO gene sets from the MSigDB Molecular Signatures Database. The Hallmark (H) gene sets represent well-defined biological states or processes, whereas the GO (C5) set consists of genes annotated by the same ontology term.

2025-12-14 | E-MTAB-16151 | biostudies-arrayexpress

WG-DASL expression profiling of formalin-fixed paraffin embedded primary breast tumours and matched lymph node metastases across four clinically relevant metastatic groups

Project description:The development of metastases is a complex multi-step process manifested by diverse patterns, involving single or multiple organs and different time-courses of distant recurrences. The aim of this study was to characterise molecular patterns associated with patterns of organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases. This study includes patients with four patterns of first metastatic sites: bone only (with no visceral metastases within 6 months of first metastasis); to viscera only (with no bone metastasis within 6 months of first metastasis); to bone and visceral organs within a 6 month period; and no recorded distant metastasis. The study population was composed of 5,061 patients diagnosed with invasive primary breast cancer without distant metastasis at the time of diagnosis between 1975 and 2005 from Guyâs Hospital. From the study population, an incidence-based case-control design was used to include patients from each of the metastatic groups and a control series randomly matched to cases according to having no reported metastasis up to the calendar date of metastasis. The aim of this expression profiling study was to characterise any molecular patterns that may be associated with the organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases.

2017-12-01 | E-MTAB-4003 | biostudies-arrayexpress

MethylationEPIC - Epigenetic Activation of AKT1 Drives Metabolic Reprogramming in Advanced-Stage Lipedema: A Multi-Omics Study

Project description:Lipedema is a chronic, progressive adipose disorder affecting predominantly women, characterized by painful, symmetrical accumulation of subcutaneous fat in the limbs, and typically resistant to diet or exercise. The underlying pathophysiology of advanced stages remains poorly defined, and no validated biomarkers or molecular targets currently guide diagnosis or therapy. In this observational study, we employed a comprehensive multi-omics strategy to investigate the molecular and metabolic landscape of late-stage lipedema in female patients. Genome-wide DNA methylation profiling revealed over 5,000 differentially methylated CpG sites, impacting genes involved in receptor tyrosine kinase signaling, phospho-metabolism, and immune regulation. Transcriptome analysis identified pronounced downregulation of mitochondrial functions, including oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, and fatty acid β-oxidation, along with sirtuin pathway disruption and extracellular matrix remodelling. Integrative analysis pinpointed AKT1, a serine/threonine kinase involved in metabolism and survival, as a putative central regulator. A hypomethylated promoter region in AKT1 was associated with increased gene expression and protein phosphorylation. Metabolomic profiling of adipose tissue revealed altered levels of AKT1-linked metabolites, including L-arginine, NADP, ATP, guanosine, glycerol, and glutamate, suggesting coordinated dysregulation of amino acid metabolism, redox homeostasis, and energy production. Trans-omic network analysis further confirmed AKT1 as a central metabolic hub integrating epigenetic, transcriptomic, and metabolic alterations. Our findings identify epigenetically activated AKT1 signaling as a potential pathogenic driver of metabolic reprogramming in advanced lipedema and propose AKT1 as a candidate biomarker and therapeutic target to support disease stratification and intervention strategies.

2025-08-12 | E-MTAB-15365 | biostudies-arrayexpress

Evidence of epigenetic reprogramming in bone marrow following influenza A (H1N1) infection during early life

Project description:The study explores the specific impact of early life influenza A/H1N1 infection on epigenetic programming within the bone marrow microenvironment. Using a murine model, we investigated how viral infection, occurring during the early life developmental period, can induce lasting changes in the epigenetic landscape of the bone marrow.

2025-12-31 | E-MTAB-14387 | biostudies-arrayexpress

Epigenomic characterization of patient-derived lung tumoroids using DNA methylation profiling

Project description:DNA methylation analysis of patient-derived lung tumoroids and matched healthy organoids demonstrates preservation of tumor-specific epigenomic identity during long-term culture. Tumoroids maintain the methylation landscape of their parental tumors, with samples from the same patient clustering together based on DNA methylation profiles regardless of culture conditions. Differential methylation analysis reveals distinct tumor-specific patterns distinguishing tumoroids from healthy organoids, confirming stable epigenomic preservation. These findings validate the tumoroid platform as a reliable model for precision CAR T-cell therapy development and personalized treatment testing in lung cancer.

2025-12-29 | E-MTAB-16020 | biostudies-arrayexpress

DNA methylation array datasets from patients with cutaneous melanoma as well as control specimen from benign nevi and skin

Project description:The dataset includes samples of 19 patients with cutaneous melanoma, 11 samples from donors with benign nevi as well as 11 control skin samples. All DNAs were derived from FFPE material. The cutaneous melanoma and benign nevi samples were macrodissected prior to DNA isolation. For methylation profiling the MethylationEPIC array from Illumina was used.

2024-05-15 | E-MTAB-14045 | biostudies-arrayexpress

DNA methylation analysis of phaeochromocytoma, paraganglioma and normal adrenal medulla samples

Project description:Illumina Infinium MethylationEPIC BeadChip array files from phaeochromocytoma, paraganglioma tumours of different genotypes and normal adrenal medulla control samples. This is the first study using high-resolution MethylationEPIC arrays and also includes a large number of Cluster 1 tumours (n=16) which exhibit extensive epigenetic deregulation.

2023-12-21 | E-MTAB-13433 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data