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Series GSE84897 Query DataSets for GSE84897
Status Public on Apr 28, 2017
Title Genome-wide analysis of DNA hydroxymethylation and methylation during epstein-barr virus infection.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Extensive DNA methylation in promoter regions is observed in gastric cancer with Epstein-barr virus (EBV) infection and EBV infection is the cause to induce this extensive hypermethylaiton phenotype in gastric epithelial cells. From transcriptome analysis, we found that TET2, one of the demethylase enzymes, was downregulated by EBV infection in gastric epithelial cell line MKN7. TET2 was overexpressed in a gastric epithelial cell line, GES1, to see its function and the hydroxymethylation, a byproduct of DNA demethylation, acquired genes by TET2 overexpression and methylation acquired genes by EBV infection were significantly overlapped. These suggested that hydroxymethylation by TET2 could function to keep unmethylated status of genes before EBV infection, and TET2 depression could contribute to methylation acquisition of these target genes after EBV infection.
Overall design Hydroxymethylation analysis in TET2 over expressed cell line, and methylation and transcriptome analysis in EBV infected cell lines.
Examination of 2 different histone modifications in 2 cell types.
Contributor(s) Kaneda A, Namba-Fukuyo H, Fukuyo M
Citation(s) 27829228
Submission date Jul 27, 2016
Last update date May 15, 2019
Contact name Masaki Fukuyo
Organization name Chiba University
Department Department of Molecular Oncology
Street address 1-8-1 Inohana, Chuo-ku
City Chiba
ZIP/Postal code 260-8670
Country Japan
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (8)
GSM2253669 GES1_TET2OE_hMeDIPseq
GSM2253670 GES1_Mock_hMeDIPseq
GSM2253671 GES1_WT_MeDIPseq
BioProject PRJNA335645
SRA SRP079995

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Supplementary file Size Download File type/resource
GSE84897_RAW.tar 1.3 Gb (http)(custom) TAR (of BIGWIG, GTF, XLSX)
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Raw data are available in SRA
Processed data provided as supplementary file

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