|
Status |
Public on Aug 09, 2013 |
Title |
Colon_Primary_Normal |
Sample type |
SRA |
|
|
Source name |
primary colon adjacent to tumor tissue, matching control for tumor; BioChain Institute, INC(Catalog no D8235090-pp-10, lot no A704198)
|
Organism |
Homo sapiens |
Characteristics |
disease type: None culture medium and passage number: NA race: NA gender: male cogdx (cognitive impairment): NA gpath (global pathology): NA nft (neurofibrillary tangles): NA np (neuritic plaques): NA age at death: 81
|
Treatment protocol |
NA
|
Growth protocol |
NA
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011)
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
original data source: Meissner Lab in house
|
Data processing |
BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010). Genome_build: hg19 Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column
|
|
|
Submission date |
Aug 08, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Michael Johannes Ziller |
Organization name |
Max Planck Institute of Psychiatry
|
Department |
Translational Psychiatry
|
Lab |
Ziller lab
|
Street address |
Kraepelinstrasse 2-10
|
City |
Munich |
ZIP/Postal code |
80804 |
Country |
Germany |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE46644 |
Charting a dynamic DNA methylation landscape of the human genome |
|
Relations |
Reanalyzed by |
GSE79801 |
BioSample |
SAMN02313887 |
SRA |
SRX332737 |