|
| Status |
Public on Aug 09, 2013 |
| Title |
Colon_Tumor_Primary |
| Sample type |
SRA |
| |
|
| Source name |
colon primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease type: moderately differentiated adenocarcinoma
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: NA
|
| 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 |
SAMN02313886 |
| SRA |
SRX332736 |
