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Sample GSM927075 Query DataSets for GSM927075
Status Public on May 23, 2012
Title RWPE1-ERG HiC (library 1)
Sample type SRA
 
Source name RWPE1-ERG prostate epithelial cell line
Organism Homo sapiens
Characteristics cell line: RWPE1
cell type: benign prostate epithelial cells
overexpressing: truncated ERG
passages: 20
library: 1
Growth protocol All cells were grown in medium following ATCC recommended conditions. Briefly, the base medium for this cell line is provided by Invitrogen (GIBCO) as part of a kit: Keratinocyte Serum Free Medium (K-SFM), Kit Catalog Number 17005-042. This kit is supplied with each of the two additives required to grow this cell line (bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF) at the following concentrations: 0.05 mg/ml BPE - provided with the K-SFM kit. 5 ng/ml EGF - provided with the K-SFM kit.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using phenol/chloroform and Qiagen MinElute extraction. All library constructions were generated following recommended protocols and reagents from Illumina.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
 
Description RWPE1 cell line stably over-expressing truncated ERG encoded by the most common TMPRSS2-ERG isoform.
Data processing Library strategy: HiC
HiC: Base-calling was done using the standard Illumina pipeline. We aligned the two ends of the 54bp paired reads separately to the reference human genome hg18 using the BWA aligner. Reads mapped ambiguously to multiple locations on the genome were discarded. We further used an in-house pipeline and filtered out clonal reads caused by PCR artifacts based on the 5' and 3' read positions, removed non-ligated DNA fragments, and retained interactions with consistent expected placement relative to HindIII enzyme digestion sites.
Genome_build: hg18
Supplementary_files_format_and_content: BED: Intra-chromosomal interactions in UCSC BED format (http://genome.ucsc.edu/FAQ/FAQformat#format1). Interactions are merged from all replicates.
Supplementary_files_format_and_content: SIF: Inter-chromosomal interactions; each row consists of the start and end coordinates of each paired-end read. Interactions are merged from all replicates.

Processed data files are linked to the Series record as supplementary files.
 
Submission date May 03, 2012
Last update date May 23, 2013
Contact name David Soong
Organization name Weill Cornell Medical College
Department Institute for Computational Biomedicine
Street address 1305 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL10999
Series (1)
GSE37752 Oncogene-Mediated Alterations in Chromatin Conformation
Relations
SRA SRX145847
BioSample SAMN00990806

Supplementary data files not provided
Raw data provided as supplementary file
Processed data is available on Series record

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