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Sample GSM2195103 Query DataSets for GSM2195103
Status Public on Oct 28, 2016
Sample type SRA
Source name RWPE1
Organism Homo sapiens
Characteristics cell line: RWPE1
cell type: normal prostate
antibody: Anti-ERG Clone 9FY Biocare # CM421 C
Growth protocol VCaP cells were grown in DMEM media (Mediatech-cellgro) with 10%FBS and 1% penicillin/streptomycin. RWPE1 cells stably expressing either wild type (WT) or point mutant (P436A) of ERG were grown in Keratinocyte SFM media supplemented with bovine pitutiary extract, human recombinant epidermal growth factor, penicillin/streptomycin, and selection agents (puromycin/hygromycin)
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 NextSeq 500
Data processing Casava1.8.2 software was used for basecalling
Reads were aligned to Homo sapiens Genome (UCSC Hg19) using 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 Jun 09, 2016
Last update date May 15, 2019
Contact name Vivekananda Kedage
Organization name Indiana University
Street address 1001 E. third Street
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
Platform ID GPL18573
Series (1)
GSE73616 An interaction with Ewing's sarcoma breakpoint protein EWS defines the subset of ETS factors rearranged in prostate cancer
BioSample SAMN05219966
SRA SRX1835121

Supplementary file Size Download File type/resource
GSM2195103_ERG-ChIP_RWPE1-ERG_WT_Rep1_Peaks.txt.gz 18.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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