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Sample GSM1899559 Query DataSets for GSM1899559
Status Public on Oct 28, 2016
Title VCaP input 1
Sample type SRA
 
Source name VCaP Prostate cancer cell line
Organism Homo sapiens
Characteristics cell line: VCaP
cell type: prostate cancer
antibody: none
Treatment protocol None
Growth protocol VCaP cells were grown in DMEM media (Mediatech-cellgro) with 10%FBS and 1% penicillin/streptomycin
Extracted molecule genomic DNA
Extraction protocol ChIP DNA was extracted as described in Hollenhorst et al., Genes and Dev. 2011
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Vertebral-Cancer of the Prostate (VCaP)
Data processing Casava1.8.2 software was used for basecalling
Reads were aligned to Homo Sapien Genome (UCSC Hg19) uisng Bowtie2 (v0.12.8)
Peaks were called using Useq program (v8.4.0)
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab delimited text files with chromosome:start-end
 
Submission date Sep 30, 2015
Last update date May 15, 2019
Contact name Vivekananda Kedage
E-mail(s) vkedage@indiana.edu
Organization name Indiana University
Street address 1001 E. third Street
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
 
Platform ID GPL11154
Series (1)
GSE73616 An interaction with Ewing's sarcoma breakpoint protein EWS defines the subset of ETS factors rearranged in prostate cancer
Relations
BioSample SAMN04123712
SRA SRX1297356

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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