Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [I]

ABSTRACT: In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Total RNA was isolated from 2 human tissues (liver and small intestine) and 3 human hepatoma cells that were treated with or without 5-aza-2’-deoxycytidine, and used for mRNA expression analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Wataru Habano

PROVIDER: E-GEOD-67318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [II]

Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 7 samples were hybridized to the Illumina HumanMethylation450 BeadChip.

2015-06-16 | E-GEOD-67477 | biostudies-arrayexpress

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-16 | E-GEOD-67485 | biostudies-arrayexpress

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [III]

2015-06-16 | GSE67484 | GEO

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [II]

2015-06-16 | GSE67477 | GEO

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [I]

2015-06-16 | GSE67318 | GEO

Global DNA methylation landscape reveals roles of DNA methylation involved in the regulation of drug metabolizing enzyme [III]

Project description:In order to elucidate the role of DNA methylation in the DME gene regulation, global DNA methylation and mRNA expression profiles of human tissues and cell lines were examinde by HumanMethylation450 Bead Chip and SurePrint G3 Human Gene Expression 8×60K v2. We demonstrated DNA methylation landscape of the DME genes in human tissues. Although a fraction of DME genes can be regulated by their DNA methylation, the variable DNA methylation status probably affects drug metabolism and response. Bisulphite converted DNA from the 4 samples were hybridized to the Illumina HumanMethylation450 BeadChip (Sample L and SI were examined twice).

2015-06-16 | E-GEOD-67484 | biostudies-arrayexpress

Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [RNA-seq]

Project description:Cytosine methylation is a reversible epigenetic modification to DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DME family of 5-methylcytosine DNA glycosylases. Demethylation by DME is critical for seed development. Consequently, determining the function of the entire gene family in somatic tissues by mutant analysis has not been possible. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; dml3 (drdd) leaves exhibit hypermethylated genomes compared to both wild-type plants and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which is correlated with 5’ hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation patterning across somatic tissues and defines the epigenetic landscape of both intergenic and coding regions.

2021-12-27 | GSE191304 | GEO

Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time [BiSulfite-seq]

2021-12-27 | GSE191006 | GEO

Analysis of the expression of Ataxin-2-target genes

Project description:We recently identified the RNA targets of Ataxin-2 by using PAR-CLIP. To elucidate the functional role of Ataxin-2 on target-binding, we have knocked down or overexpressed Ataxin-2 in HEK293T cells and extracted RNAs 48 hrs after transfection. Then, these total RNAs were subjected to whole transcripts microarray analysis to examine how the perturbation of Ataxin-2 expression affects target gene expression. Ataxin-2 was either knocked down using siRNA or overexpressed using the expression construct of Halo-Ataxin-2.Control siRNA was transfected as a control of knockdown experiment. The expression construct of Halo-tag alone was used as a control of overexpression experiment. Forty-eight hrs after transfection, total RNAs were extracted and subjected to microarray analysis.

2014-06-20 | E-GEOD-53189 | biostudies-arrayexpress

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance (BS_Seq)

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in Col-0,rdd-2,dme single mutants(dme-A-del,dme-T-In,dme-3-In,dmeDD7 pro) and quadruple mutants(drdd+395 pro and drddDD7 pro)

2021-01-16 | GSE164914 | GEO

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