Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic analysis of gastric cancer

ABSTRACT: Genome-wide DNA methylation profiling of gastric tumors and matched gastric non-malignant samples. The Illumina HumanMethylation27 BeadChip was used to obtain DNA methylation profiles across 27,578 CpGs in 203 gastric tumors and 94 matched non-malignant gastric samples.

ORGANISM(S): Homo sapiens

PROVIDER: GSE30601 | GEO | 2012/10/24

SECONDARY ACCESSION(S): PRJNA144547

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epigenetic analysis of gastric cancer

Project description:Genome-wide DNA methylation profiling of gastric tumors and matched gastric non-malignant samples. The Illumina HumanMethylation27 BeadChip was used to obtain DNA methylation profiles across 27,578 CpGs in 203 gastric tumors and 94 matched non-malignant gastric samples. Bisulphite-converted DNA from the 203 gastric tumors and 94 matched gastric non-malignant samples was hybridized to the Illumina HumanMethylation27 BeadChip.

2012-10-24 | E-GEOD-30601 | biostudies-arrayexpress

Methylation profiles of lung adenocarcinoma patients in Taiwan

Project description:Genome wide DNA methylation profiling of tumor samples with lung adenocarcinoma patients. The Illumina HumanMethylation27 BeadChip array was used to obtain DNA methylation profiles across approximately 27,578 CpGs in lung cancer samples. Samples included tumor samples with lung adenocarcinoma.

2017-02-09 | GSE83845 | GEO

Genetic Landscape of Copy Number Alterations in Gastric Cancer

2012-02-10 | GSE31168 | GEO

Genetic Landscape of Copy Number Alterations in Gastric Cancer

Project description:Genome-wide DNA copy number profiling of gastric tumors and matched non-maligant samples. The affymetrix SNP6 array was used to obtain DNA copy number profiles in 193 gastric tumors and 98 matched gastric non-malignant samples. Genomic DNA extracted from 193 gastric tumors and 98 matched gastric non-malignant (normal) tissues was hybridized on Affymetrix SNP6 genotyping arrays.

2012-02-10 | E-GEOD-31168 | biostudies-arrayexpress

Methylation Pattern of Human Dermal Fibroblasts

Project description:In this study, we have analyzed DNA methylation changes upon aging of human dermal fibroblasts by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were isolated from skin samples donated by young (6-23 years) and elderly (60-73 years) patients undergoing surgical interventions. Strikingly, global DNA-methylation profiles of fibroblasts from the same anatomical site clustered closely together indicating that fibroblasts maintain positional memory even after in vitro culture.

2012-02-14 | GSE22595 | GEO

Genome wide DNA Methylation Study in Cornelia de Lange Syndrome

Project description:Differential DNA methylation was identified in CdLS, and correlates to cohesin binding as well. However, DNA methylation may only be one of several events that regulate gene expression in humans. 63 Lymphoblastoid cell lines (LCLs) from 39 CdLS probands, 2 RBS probands and 22 gender and racial matched healthy controls were tested on HumanMethylation27 DNA Analysis BeadChip (Illumina) which carries 27,578 highly informative CpG sites derived from the well-annotated NCBI CCDS database

2010-07-07 | E-GEOD-18458 | biostudies-arrayexpress

A signature predicting poor prognosis in gastric and ovarian cancer represents a coordinated macrophage and stromal-response.

Project description:Genome wide mRNA expression profiling of 94 gastric tumours derived from Australian based cohort was performed. . From this data we identified a cluster of co-expressed genes termed the stromal response cluster which almost perfectly differentiates tumor from its non-malignant gastric tissue and hence can be regarded as a highly tumor-specific gene expression signature. We show that these genes are consistently co-expressed across a range of independent gastric datasets as well as other cancer types suggesting a conserved functional role in cancer. Profiling of 94 primary gastric tumors on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. All tumors were collected with approvals from Peter MacCallum Cancer Center, Australia; the Research Ethics Review Committee; and signed informed patient consent.

2014-04-01 | E-GEOD-51105 | biostudies-arrayexpress

The DNA methylomes of serous borderline tumours reveal subgroups with malignant-like or benign-like profiles

Project description:Serous borderline tumours (SBOT) are a challenging group of ovarian tumours positioned between benign and malignant disease. We have profiled the DNA methylomes of 12 low grade serous carcinoma (LGSC), 19 SBOT and 16 benign serous tumours (BST) across 27,578 CpG sites to further characterise the epigenomic relationship between these subtypes of ovarian tumours. Unsupervised hierarchical clustering of DNA methylation levels showed that LGSC differ distinctly from BST, however, not from SBOT. Gene ontology analysis of genes showing differential methylation at linked CpG sites between LGSC and BST revealed significant enrichment of gene groups associated with cell adhesion, cell-cell signalling and the extracellular region consistent with a more invasive phenotype of LGSC as compared to BST. Consensus clustering highlighted differences between SBOT methylomes and returned subgroups with malignant-like or benign-like methylation profiles. Furthermore, a two loci DNA methylation signature can distinguish between these SBOT subgroups with benign-like and malignant-like methylation characteristics. Our findings indicate striking similarities between SBOT and LGSC methylomes which supports a common origin and the view that LGSC may arise from SBOT. A subgroup of SBOT can be classified into tumours with a benign-like or a malignant-like methylation profile which may help in identifying tumours more likely to progress into LGSC. Array-based methylation profiling was performed using the Infinium HumanMethylation27 BeadChip in 12 low grade serous carcinoma, 19 serous borderline tumours and 16 benign serous tumours. The reproducibility of the Infinium HumanMethylation27 BeadChips was evaluated using four biological replicates of the high grade serous ovarian cancer cell line PEO1. Differential methylation cutoff was estimated from four biological replicates by bootstrap resampling and set at Δβ ≥ 0.25 corresponding to a FDR ≤ 0.09.

2012-12-31 | E-GEOD-40105 | biostudies-arrayexpress

Methylation Pattern of Human Mesenchymal Stromal Cells

Project description:In this study, we have analyzed DNA methylation changes upon long-term culture and aging of MSC by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.Overall, the methylation pattern was maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites. Notably, methylation changes in MSC were related in long-term culture and aging in vivo.

2010-02-04 | GSE17448 | GEO

DNA Methylation Analysis in Human Chorionic Villus and Maternal Blood Cells

Project description:Comparative analysis of DNA methylation in 12 human chorionic villus samples and 12 human maternal blood cell samples We performed a genome wide analysis of DNA methylation first trimester CVS samples and gestational age matched MBCs. We analyzed DNA samples obtained from 12 CVS samples and 12 MBC samples. Data were generated using two high-throughput approaches: the Infinium “humanmethylation27” platform marketed by Illumina and a custom Agilent-based platform. We then compared these data with genome wide transcription data for the same tissues. This Series covers only the Illumina HumanMethylation27 part of the study.

2010-07-31 | E-GEOD-23311 | 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