|
| Status |
Public on Sep 01, 2015 |
| Title |
1154337-RRBS-GC |
| Sample type |
SRA |
| |
|
| Source name |
gastric cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric cancer cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard DNA extraction protocol using QIAamp DNA Micro Kit
RRBS libraries were prepared according to Meissner's protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
gastric cancer cells
|
| Data processing |
Base calling was performed throughout methylation specific mapping tool, BRAT software for short bisulfite treated reads because unmethylated cytosine within sequenced read from RRBS technique is converted into thymine.
RRBS of same normal tissue was carried out twice due to a small amount.
Regions of promoter known as primary candidate of epigenetic regulation were selected for consequential analysis focusing differentially methylated promoters (DMPs).
Methylated and unmethylated CpGs were counted and enrichment test (Fisher's exact test) was used about methylated frequency during gastric carcinogenesis with 2 by 3 contigency table.
DMPs having 3 or more significant CpG sites were selected as prospective candidates.
Genome_build: hg18
Supplementary_files_format_and_content: bed files include methylated and unmethylated read count of individual CpG sites. RRBS method provides single base pair resolution data of methylation signal in C of CpG site.
|
| |
|
| Submission date |
Feb 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hee-jin Kim |
| E-mail(s) |
heejin@kribb.re.kr
|
| Organization name |
KRIBB
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
363-883 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE55159 |
Epigenome signatures during gastric carcinogenesis based on next generation sequencing analysis [Bisulfite-Seq] |
| GSE55160 |
Epigenome signatures during gastric carcinogenesis based on next generation sequencing |
|
| Relations |
| BioSample |
SAMN02646654 |
| SRA |
SRX474007 |
