Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenome analysis of primary intracranial sarcoma

ABSTRACT: Genome wide DNA methylation profiling of DNA extracted from formalin-fixed parffin embedded tumor samples from patients with primary intracranial sarcoma from Peru. The Illumina MethylationEPIC array was used to obtain DNA methylation profiles of 850.000 CpG sides

ORGANISM(S): Homo sapiens

PROVIDER: GSE155660 | GEO | 2021/09/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Epigenome analysis of intracranial mesenchymal tumors with FET-CREB fusions

Project description:Genome-wide DNA methylation profiling of 20 intracranial mesenchymal tumors with FET-CREB fusions encompassing both intracranial myxoid mesenchymal tumors and intracranial angiomatoid fibrous histiocytoma-like neoplasms. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 20 intracranial mesenchymal tumors with FET-CREB fusions.

2021-11-18 | GSE164994 | GEO

Epigenome analysis of formalin-fixed paraffin-embedded (FFPE) meningioma samples

Project description:Genome wide DNA methylation profiling of formalin-fixed paraffin-embedded (FFPE) meningioma samples. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 methylation sites across the genome at single-nucleotide resolution.

2022-04-27 | GSE200321 | GEO

Genome-wide DNA methylation profiles of endometrioid endometrial cancer tissue

Project description:Genome-wide DNA methylation screening was performed using the Infinium MethylationEPIC BeadChip in 49 fresh-frozen tissue samples and 31 formalin-fixed paraffin-embedded tissue samples obtained from surgically resected materials of patients with endometrioid endometrial cancer.

2022-11-09 | GSE178610 | GEO

Methylation profiling (450K and EPIC array) for sarcoma classification

Project description:Infinium® HumanMethylation450 BeadChip and EPIC arrays were run with the aim of using the methylation profiles (n=986 in total) for sarcoma subtype classification (Paper: Lyskjær et al, 2021, DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the ‘DKFZ sarcoma Classifier’ ). 500ng of DNA from fresh frozen (FT) or formalin-fixed paraffin-embedded (FFPE) tumour samples were bisulfite converted using the Zymo EZ DNA methylation Gold kit (Zymo Research Corp. Irvine, USA) before hybridisation to the Infinium HumanMethylation450 or EPIC beadchip arrays (Illumina, San Diego, CA) by UCL Genomics. All bisulfite-converted FFPE samples were restored with the Infinium FFPE DNA Restore kit (Illumina).

2021-05-01 | E-MTAB-9875 | biostudies-arrayexpress

Epigenome analysis of primary intracranial sarcoma

Project description:Epigenome analysis of primary intracranial sarcoma

| PRJNA655144 | ENA

Methylation profiling of Desmoplastic myxoid tumor

Project description:Atypical teratoid/rhabdoid tumor (ATRT) is a highly malignant brain tumor predominantly occurring in infants. Mutations of the SMARCB1 gene are the characteristic genetic lesion. We characterized a series of SMARCB1-deficient intracranial tumors sharing distinct clinical, histopathological and molecular features. Median age of the four females and three males was 40 years (range: 15-61 years). All tumors were located in the pineal region. Histopathologically, these tumors displayed spindled and epithelioid cells embedded in a desmoplastic stroma alternating with a variable extent of a loose myxoid matrix. All cases showed loss of nuclear SMARCB1/INI1 protein expression. After DNA isolation from formalin-fixed paraffin-embedded tumor samples, purification and bisulfite conversion using standard protocols provided by the manufacturer, all samples were analyzed using the HumanMethylation450 BeadChip array or the MethylationEPIC BeadChip array (Illumina Inc., San Diego, CA). Six samples passed initial quality control and were further analyzed. Most DNA methylation profiles were not classifiable using the Heidelberg Brain Tumor Classifier (version v11b4). On unsupervised t-SNE analysis and hierarchical clustering analysis, however, all tumors grouped closely together and showed similarities with ATRT-MYC.

2019-10-01 | GSE138221 | GEO

DNA methylation in sarcoma patients

Project description:We retrospectively identified adult patients who had received anti-PD-1 ICI therapy for recurrent sarcoma and performed DNA methylation profiling using Infinium MethylationEPIC microarrays. Response to anti-PD-1 ICI therapy was correlated with DNA methylation profiles.

2021-04-21 | GSE172468 | GEO

Epigenome analysis of intracranial aneurysm and superficial temporal artery samples

Project description:Genomic DNA of intracranial aneurysm and matched superficial temporal artery from same patient (n=9) was extracted with QIAamp DNA Mini Kit (Qiagen, Valencia, CA). A total of 500 of genomic DNA was bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA) and then analyzed on an Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA) following the manufacturer’s instructions.

2016-12-01 | GSE75434 | GEO

Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (EPIC)

Project description:DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. We also performed analysis on the EPIC array with paired FF and FFPE samples, to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array.

2017-04-01 | GSE92579 | GEO

Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (450K)

2017-04-01 | GSE92577 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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