Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays

ABSTRACT: To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE47637 | GEO | 2013/06/05

SECONDARY ACCESSION(S): PRJNA207000

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide DNA methylation profiling of KYSE180 cells transfected with HOTAIR vector using Illumina HumanMethylation 450 arrays

Project description:To analysis of the effect of HOTAIR on global DNA methylation in KYSE180 esophageal cancer cell line, genome-scale DNA methylation was analyzed in a pair of esophageal cancer cell lines, KYSE180 cells stably transfected with HOTAIR and control KYSE180 cells. The results from genome-wide DNA methylation analysis indicate that hypermethylation occurs more frequently than hypomethylation after stably ectopic expressing HOTAIR in KYSE180 cells. DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacture's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value. For pairwise differential methylation analysis, the difference of two biological replicates of the ESCC cell lines KYSE180 and KYSE180_HOTAIR was calculated.

2013-06-05 | E-GEOD-47637 | biostudies-arrayexpress

Genome-wide methylation analysis of esophageal mucosa using Infinium HumanMethylation 450 BeadChip

Project description:DNA methylation in esophageal mucosae with cancer risk

2018-02-28 | GSE77991 | GEO

Genome-wide methylation analysis of esophageal squamous cell carcinoma using Infinium HumanMethylation 450 BeadChip

Project description:DNA methylation in esophageal squamous cell carcinoma (ESCC)

2016-06-30 | GSE74693 | GEO

Genome-wide methylation analysis of esophageal squamous cell carcinoma using Infinium HumanMethylation 450 BeadChip

Project description:DNA methylation in esophageal squamous cell carcinoma (ESCC) A picture of epigenetic alterations in ESCCs was characterized.

2016-06-30 | E-GEOD-74693 | biostudies-arrayexpress

HOTAIR reprograms gene expression profiling in esophageal squamous cell carcinoma (ESCC) KYSE180 cells

2013-06-05 | GSE47638 | GEO

HOTAIR reprograms gene expression profiling in esophageal squamous cell carcinoma (ESCC) KYSE180 cells

Project description:To investigate the functional role of HOTAIR in esophageal squanmous cell carcinoma (ESCC) cells, RNAi-mediated knockdown of HOTAIR and overexpression of HOTAIR were carried out using KYSE180 cells. Gene expression microarray analysis revealed that a number of reported HOTAIR target genes were regulated by HOTAIR. Moreover, gene ontology analysis revealed enrichment of genes closely related to tumorigenesis, such as cell migration, regulation of cell cycles. For RNAi-mediated knockdown of HOTAIR, two different stealth siRNAs against HOTAIR were generated by Invitrogen, after which a mixture of the two was used for transfection. KYSE180 cells in 6-well plates were transfected with 100 pmol of Stealth siRNA (Invitrogen) or a Stealth RNAi Negative Control Medium GC (Invitrogen) using Lipofectamine2000 (Invitrogen). For HOTAIR overexpression, KYSE180 cells were transfected with LZRS_HOTAIR vector using Polyfect Transfection Reagent (Qiagen). Total RNA was extracted 48 h after transfection.

2013-06-05 | E-GEOD-47638 | biostudies-arrayexpress

Genome-wide methylation analysis of ependymoma using Infinium HumanMethylation 450 BeadChip

Project description:Genome wide DNA methylation profiling of ependymomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 83 ependymomas.

2018-05-17 | GSE114523 | GEO

Genome-wide methylation analysis of PCNSL using Infinium HumanMethylation 450 BeadChip

Project description:Genome wide DNA methylation profiling of primary CNS lymphomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 95 primary CNS lymphomas and 2 metastatic DLBCLs in CNS.

2017-04-01 | GSE92676 | GEO

Genome-wide methylation analysis of gastric mucosae using Infinium HumanMethylation 450 BeadChip

Project description:DNA methylation in gastric mucosae

2019-12-23 | GSE92863 | GEO

Genome-wide methylation profiles in saliva and intestinal mucosa using Infinium HumanMethylation 450 BeadChip

Project description:Genome wide DNA methylation profiling in paired saliva and intestinal mucosa samples from individuals undergoing gastroscopies. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The aim of the study was to determine the utility of saliva as a surrogate for intestinal mucosa in DNA methylation studies.

2019-02-07 | GSE118260 | 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