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Sample GSM353622 Query DataSets for GSM353622
Status Public on May 18, 2010
Title VCaP_regular_medium_Pan_H3
Sample type SRA
Source name VCaP - regular medium - Chromatin IP against Pan-H3
Organism Homo sapiens
Characteristics regular medium
Growth protocol Prostate cell lines were maintained in appropriate medium. For androgen treatment experiment, LNCaP and VCaP cells were hormone starved for 48 hours prior to treatment with ethanol control or synthetic androgen R1881. For RNA interference of ERG, VCaP cells were grown in regular medium and subjected to non-silencing control siRNA or siRNA specific for targeting ERG on two continuous days. At 48 hour after the last siRNA transfection, cells were harvested for ChIP analysis.
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description Chromatin IP against Pan-H3
Data processing Reads were aligned to the reference genome using Eland software (Illumina). Enriched intervals were identified by a Hidden Markov Model-based program named HPeak (Qin et al. unpublished).
Submission date Dec 22, 2008
Last update date May 15, 2019
Contact name Jindan Yu
Organization name Northwestern University
Department Medicine - Hem/Onc
Lab Yu
Street address 303 E. Superior St.
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platform ID GPL9052
Series (2)
GSE14092 An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression (II)
GSE14097 An Integrated Network of Androgen Receptor and TMPRSS2-ERG Gene Fusion in Prostate Cancer Progression
SRA SRX022556
BioSample SAMN00016569

Supplementary file Size Download File type/resource
GSM353622_20E46AAXX_CS36.allregions.txt.gz 22.2 Kb (ftp)(http) TXT
GSM353622_s_6_export.txt.gz 297.7 Mb (ftp)(http) TXT
GSM353622_s_8_eland_result.txt.gz 240.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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