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

Global epigenomic profiling of corticotroph pituitary neuroendocrine tumors

ABSTRACT: Corticotroph pituitary neuroendocrine tumors (PitNETs) are heterogeneous sellar neoplasms with variable clinical manifestations and growth behaviour. In this study, epigenomic data was generated as part of an integrative meta-analysis of corticotroph PitNETs, which included epigenomic, transcriptomic, and proteomic investigations. This deposit comprises idat files of tumor samples and adenohypophysial non-neoplastic control samples. These data were integrated with previously published external molecular datasets. The combined analyses defined four clinically relevant molecular subgroups of corticotroph PitNETs.

ORGANISM(S): Homo sapiens

SUBMITTER: Matthias Dottermusch

PROVIDER: E-MTAB-16589 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic and metabolic rewiring in metastatic pheochromocytomas and paragangliomas driven by SDHB mutations (DNA methylation data)

Project 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.

2025-12-23 | E-MTAB-15178 | 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 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

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

Genomic analysis of low-grade serous ovarian carcinomas [ILOEF]

Project description:Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted.We sought to identify differences in genomic copy number changes between co-existing borderline and invasive components of serous carcinoma. Paired co-existing borderline and invasive tumor components were sampled and profiled from formalin-fixed paraffin embedded tumors from 6 patients

2014-10-01 | E-GEOD-57276 | biostudies-arrayexpress

Genome-wide methylation profiling of sporadic Pancreatic Neuroendocrine Tumors

Project description:Pancreatic neuroendocrine tumors (PanNETs) account for 1-3% of all neoplasms of the pancreas. Epigenetic changes seem to be the main drivers of PanNET tumorigenesis. Indeed, the most frequent mutated genes in PanNETs are DAXX (Death domain associated protein 6), ATRX (Transcriptional Regulator ATRX) and MEN1 (menin 1), which are all involved in epigenetic regulation. The objective of the project is to study the epigenetic changes undergoing in PanNETs. Specifically, we aimed at investigating whether do exist biologically important epigenetic differences in PanNET, useful for a clinically relevant classification.

2022-11-30 | E-MTAB-11962 | biostudies-arrayexpress

Genome-wide methylation profiling of sporadic Pancreatic Neuroendocrine Tumors

2022-11-30 | E-MTAB-11965 | biostudies-arrayexpress

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

Epigenomic profiling of Glioblastoma Stem Cells (U3117) subjected to TET1, TET2 or TET3 protein knockouts and subsequent treatment with ascorbic acid.

Project description:Glioblastoma (GBM) is a fatal disease with a poor prognosis, whose aetiology involves profound molecular alterations. Given the limited progress made in recent years, research into new therapeutic avenues may improve the treatment of GBM patients. In this work, we have characterised the epigenomic landscape of patient-derived glioblastoma stem cells in the context of a proneural GBM subtype (U31117). We performed a systematic knockdown of each of the TET proteins (TET1, TET2 and TET3) and explored the consequences of their deletion at the level of DNA methylation (5mC) and hydroxymethylation (5hmC). Global 5hmC levels were then restored using a low dose of ascorbic acid, and the epigenetic landscape of all these conditions was examined using high-content DNA methylation microarrays (Illumina MethylationEPIC Beadchip platform).

2024-12-31 | E-MTAB-13504 | biostudies-arrayexpress

Integrated Fibre-Specific Methylome and Proteome Profiling of Human Skeletal Muscle Across Males and Females with Fibre-Type Deconvolution.

Project description:We simultaneously extracted DNA and protein from >200 single fibres per participant (7 males, 5 females) to directly compare methylome and proteome profiles of Type I and Type II human skeletal muscle fibres. Using the EPICv2 array and LC-MS/MS, we identified 5,689 robust DMRs (FDR <0.001) and 338 DEPs (FDR <0.001), revealing strong inverse correlations between methylation and protein abundance in key contractile and metabolic genes. We also built a TI/TII DNA methylation reference matrix and implemented fibre-type deconvolution (MyoTYPE) for whole-muscle samples, all accessible via the MyoMETH web resource.

2025-10-13 | PXD066393 | Pride

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