|
| Status |
Public on Jul 03, 2013 |
| Title |
Benign Prostate Tissue 1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: Benign, prostate tissue
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from primary human samples, digested with MspI restriction enzyme (200U MspI per reaction), subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors (T4 DNA ligase). Fragments of 150-400 bp were isolated after agarose gel electrophoresis and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers (18 cycles). Libraries were sequenced using an Illumina HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read runs.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences using FAR software and then mapped to hg18 whole genome using the bismark alignment software with a maximum of 2 mismatches in a directional manner. Only uniquely aligning reads were retained
Methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (or per base)
|
| |
|
| Submission date |
Oct 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Pei-Chun Lin |
| E-mail(s) |
pel2008@med.cornell.edu
|
| Phone |
(212)746-6306
|
| Fax |
(212)746-8816
|
| Organization name |
Cornell Weill Medical College
|
| Department |
Pathology and Laboratory Medicine
|
| Lab |
Dr. Mark A. Rubin
|
| Street address |
1300 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE41701 |
Epigenomic alterations in localized and advanced prostate cancer |
|
| Relations |
| SRA |
SRX197540 |
| BioSample |
SAMN01773193 |
