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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

ABSTRACT: To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines

ORGANISM(S): Homo sapiens

PROVIDER: GSE46595 | GEO | 2016/03/28

SECONDARY ACCESSION(S): PRJNA201424

REPOSITORIES: GEO

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines MBD sequencing of normal tissue (n), purified gastric cancer (sc), and cultured gastric cancer cell (dc) were generated by deep sequencing, in five samples from three patients (csc1, csc2, csc3) and two replicates (csc1_sc2, csc1_sc3), using Illumina GAIIx.

2016-03-28 | E-GEOD-46595 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer.

Project description:Abnormal DNA methylation is an epigenetic mechanism that promotes gastric carcinogenesis. While the abnormal methylation at promoter regions has been characterized for many genes, the function of DNA methylation marks at distal regulatory regions in gastric cancer remains poorly described. Here, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines to understand the epigenetic changes in the distal as well as the proximal regulatory regions. In total, 257,651 significant DMRs (Differentially methylated regions) were identified in gastric cancer, and the majority of these DMRs were located in the intergenic, intronic, and non-coding RNA regions. We identified the aberrant expression of many genes and lncRNAs due to changes in DNA methylation. Furthermore, we profiled the molecular subtype-specific methylation patterns in gastric cancer to characterize subtype-specific regulators that undergo DNA methylation changes. Our findings provide insights for understanding methylation changes at distal regulatory regions and reveal novel epigenetic targets in gastric cancer.

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

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

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

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

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