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

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

PROVIDER: PRJNA201422 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1041581.fastq.gz	Fastqsanger.gz
	SRR1041582.fastq.gz	Fastqsanger.gz
	SRR1041583.fastq.gz	Fastqsanger.gz
	SRR1041584.fastq.gz	Fastqsanger.gz
	SRR1041585_1.fastq.gz	Fastqsanger.gz

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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.

| S-EPMC5041931 | biostudies-literature

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.

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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.

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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

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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

2016-03-29 | E-GEOD-46598 | biostudies-arrayexpress

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

Project description:We performed H3K27ac ChIP-seq data in seven gastric cancer cell lines to investigate the functional significance of epigenetic changes at distal regulatory regions H3K27ac ChIP-seq profiling of gastric cancer cell lines were generated by deep sequencing, in each seven samples, using Illumina GAIIx and Hiseq-2000

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Project description:We performed H3K27ac ChIP-seq data in seven gastric cancer cell lines to investigate the functional significance of epigenetic changes at distal regulatory regions

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Somatic Promoter Landscape of Primary Gastric Adenocarcinoma Delineated by Epigenomic Profiling

Project description:Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic profiles of primary tumors, normal tissues, and cell lines

2016-09-28 | GSE75898 | GEO

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