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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model

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

ORGANISM(S): Homo sapiens

SUBMITTER: Joachim De Schrijver

PROVIDER: E-GEOD-45334 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [MBD-Seq]

Project description:Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained. MBD-sequencing of 8 colorectal cancer cell lines.

2013-10-01 | E-GEOD-45333 | biostudies-arrayexpress

Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [RNA-Seq]

Project description:Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained. RNA-sequencing of HCT116 cell line, the DNMT1 and DNMT3B double knock-out HCT116 cell line (DKO), and 7 additional colorectal cell lines.

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Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [MBD-Seq]

Project description:Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained.

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Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-10-01 | GSE45334 | GEO

Genome-wide total RNA and MBD-sequencing in HCT116 and DKO cells as a global re-expression model [RNA-Seq]

Project description:Genome-wide view of the interplay between methylation and RNA expression in this colorectal cancer model was obtained.

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ECSTASY (MDMA) ALTERS CARDIAC GENE EXPRESSION AND DNA METHYLATION: IMPLICATIONS FOR CIRCADIAN RHYTHM DYSFUNCTION IN THE HEART (methylation)

Project description:MDMA (ecstasy) is an illicit drug that stimulates monoamine neurotransmitter release and inhibits reuptake. MDMAâs acute cardiotoxicity includes tachycardia and arrhythmia which are associated with cardiomyopathy (CM). MDMA acute cardiotoxicity has been explored, but neither long-term MDMA cardiac pathological changes nor epigenetic changes have been evaluated. Microarray analyses were employed to identify cardiac gene expression changes and epigenetic DNA methylation changes. To identify permanent MDMA-induced pathogenetic changes, mice received daily 10d or 35d MDMA , or daily 10d MDMA followed by 25d saline washout (10+25d). MDMA treatment (10d) caused differentially gene expression (p<0.05, fold change >1.5), with 752 genes 558 genes following 35d MDMA, and 113 genes following 10d treatment +25d washout. Changes in MAPK and circadian rhythm gene expression were identified following 10d administration. After 35d, circadian rhythm genes (Per3, CLOCK, ARNTL, and NPAS2) remained differentially expressed. MDMA caused DNA hypermethylation and hypomethylation that was independent of gene expression; hypermethylation of genes was 71% at 10d, 68% at 35d, and 91% at 10+25d. Differential gene expression that corresponded directly with DNA methylation changes occurred in 22% of genes at 10d, 17% at 35d, and 48% at 10d+25d washout. MDMA treatment resulted in epigenetic changes in cardiac DNA methylation. Hypermethylation was the predominant effect. MDMA induced gene expression of key elements of circadian rhythm regulatory genes and suggest a fundamental mechanism for MDMA dysfunction in the heart. This study addresses how MDMA (ecstasy) affects cardiac (left ventricle) gene expression and epigenetic nuclear DNA methylation. Each sample was fluorescently labeled and hybridized to Roche Nimblegen 2.1M Deluxe Promoter Arrays.

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2014-02-23 | E-GEOD-54911 | biostudies-arrayexpress

DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

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MIRA-Seq analysis of bovine dermal fibroblasts from the same individuals at two different ages

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