Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

ABSTRACT: We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines. Bisulphite converted DNA from 77 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip

ORGANISM(S): Homo sapiens

SUBMITTER: Jordana Bell

PROVIDER: E-GEOD-26133 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

Project description:We measured the methylation status at 27,578 CpG sites using the Human Methylation27 DNA array in 77 HapMap Yoruba lymphoblastoid cell lines.

2011-01-05 | GSE26133 | GEO

Human Aging-associated DNA Hypermethylation Occurs Preferentially at Bivalent Chromatin Domains

Project description:There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4+ T-cells and CD14+ monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ-layer compared with blood, demonstrates that the aDMR signature is a multi-tissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoters. This same category of promoters, associated with key developmental genes, is frequently hypermethylated in cancers and in vitro cell culture, pointing to a novel mechanistic link between aberrant hypermethylation in cancer, aging, and cell culture. We measured the methylation state of 27,578 CpG sites (Illumina HumanMethylation27 array) in sorted human blood cells to validate aging-associated DMRs.

2010-06-24 | E-GEOD-20242 | biostudies-arrayexpress

BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type

2016-02-25 | E-GEOD-66285 | biostudies-arrayexpress

DNA methylation profiling of male human pancreatic islets identifies loci for type 2 diabetes

Project description:Little is known about the contribution of the epigenome to the pathophysiology of type 2 diabetes (T2D). Here we have used genome-wide DNA methylation profiling to obtain the first comprehensive DNA methylation data set for human T2D pancreatic islets. Therefore, we analyzed the methylation profile of 27,578 CpG sites affiliated to more than 14,000 genes in 16 samples of pancreatic islets, 11 normal and 5 type 2-diabetic. Keywords: DNA methylation Keywords: Methylation profiling by array We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA BeadChip array) in genomic DNA obtained from pnacreatic islets of 11 non-diabetic and 5 type-2-diabetic male human donors to identify genes that are differentially methylated in T2D.

2012-04-22 | E-GEOD-21232 | biostudies-arrayexpress

Epigenomic Analysis of Aberrantly Methylated Genes in Colorectal Cancer

Project description:Determination of the profile of genes commonly aberrantly methylated in colorectal cancer (CRC) has substantial potential value for diagnostic and therapeutic application. However, our knowledge of the DNA methylation pattern in CRC is currently limited. Therefore, we analyzed the methylation profile of 27,578 CpG sites spanning more than 14,000 genes in CRC and in adjacent normal mucosa using beadchip array-based technology. We identified 621 CpG sites located in promoter region and CpG islands that were significantly hypermethylated in CRC compared to normal mucosa. Genes on chromosome 18 showed promoter hypermethylation most frequently. According to gene ontology analysis, the most common biologically relevant class of genes affected by methylation was the class associated with the cadherin signaling pathway. In comparison with genome-wide expression array, mRNA expression was more like to be down-regulated in the genes demonstrating promoter hypermethylation, although this was not statistically significant. We validated 10 CpG sites that were shown to be hypermethylated in the array studies (ADHFE1, BOLL, SLC6A15, ADAMTS5, TFPI2, EYA4, NPY, TWIST1, LAMA1, GAS7) and 2 CpG sites showing hypomethylaion (MAEL, SFT2D3) in CRC compared to normal mucosa using pyrosequencing. The methylation status measured by pyrosequencing was consistent with the methylation array data. In conclusion, we have shown that methylation profiling based on beadchip arrays is an effective method for screening for aberrantly methylated genes in CRC. In addition, we identified novel methylated genes that are candidate diagnostic or prognostic markers for CRC. We measured the methylation status of the 27,578 CpG sites (Human Methylation27 DNA Analysis BeadChip) in 22 pairs of CRC tissue and adjacent normal mucosa to identify genes that are commonly aberrantly methylated in CRC.

2010-06-24 | E-GEOD-17648 | biostudies-arrayexpress

BLUEPRINT methylome of the HapMap cell line GM18507 (Coriell cell line NA18507)

Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line

2016-02-25 | GSE66285 | GEO

Homo sapiens strain:(YRI) Yoruba HapMap population

Project description:CompleteGenomics sequencing of (YRI) Yoruba HapMap population

| PRJNA177963 | ENA

Homo sapiens strain:(YRI) Yoruba HapMap population

Project description:Whole genome sequencing of (YRI) Yoruba HapMap population

| PRJNA33865 | ENA

DNA methylation profiling in chondrocyte dedifferentiation in vitro

Project description:Genome wide DNA methylation profiling of different passages of human articular chondrocytes treated with 5-azacytidine. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,578 CpGs.Samples included 6 different passages of human articular chondrocytes with 5-azacytidine treatment, 6 different passages without 5-azacytidine treatment, Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

2015-01-31 | E-GEOD-65467 | biostudies-arrayexpress

Differentially methylated genes in human IL-7Ra high and low EM CD8+ T cells

Project description:Genome wide DNA methylation profiling of IL-7Ra high and low EM CD8+ T cells. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,578 CpGs. Samples included 2 IL-7Ra high EM CD8+ T cells and 2 IL-7Ra high EM CD8+ T cells. Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2015-08-06 | E-GEOD-67816 | 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