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Sample GSM1022914 Query DataSets for GSM1022914
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
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
SRA SRX197540
BioSample SAMN01773193

Supplementary file Size Download File type/resource
GSM1022914_Sample_ben1.calls.txt.gz 16.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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