|
| Status |
Public on Sep 01, 2015 |
| Title |
1154337-MBD-IM |
| Sample type |
SRA |
| |
|
| Source name |
gastric intestinal metaplasia cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric intestinal metaplasia cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard DNA extraction protocol using QIAamp DNA Micro Kit
MBD libraries were prepared using Illumina ChIP Seq Sample Prep Kit according to Illumina's instructions.
|
| |
|
| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
gastric intestinal metaplasia cells
|
| Data processing |
Base-calling was performed throughout the routine process of Illumina pipeline module, bclConverter v1.7 with 76 cycles of single-read.
The sequences were aligned to the human genome assembly (hg18) using the ELAND version 2 with default parameters.
In order to evaluate the methylation peak signature, aligned coordinated were extended up to 200 bp from start position.
Read count value was converted into methylation enrichment score (MES) to remove the bias among the amount of reads from different samples.
For identification of differentially methylated regions (DMRs), sliding window approach was applied to find methylation signal difference having more than 2-fold change between samples withing 1 kb range per 200 bp bin shift.
Genome_build: hg18
Supplementary_files_format_and_content: bed files include MES values
|
| |
|
| 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) |
| GSE55157 |
Epigenome signatures during gastric carcinogenesis based on next generation sequencing analysis [MBD-Seq] |
| GSE55160 |
Epigenome signatures during gastric carcinogenesis based on next generation sequencing |
|
| Relations |
| BioSample |
SAMN02646650 |
| SRA |
SRX474003 |
