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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
fukuyo@chiba-u.jp
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| Organization name |
Chiba University
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| Department |
Department of Molecular Oncology
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| Street address |
1-8-1 Inohana, Chuo-ku
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platforms (2) |
| GPL18460 |
Illumina HiSeq 1500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA335645 |
| SRA |
SRP079995 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84897_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of BIGWIG, GTF, XLSX) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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