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Sample GSM984398 Query DataSets for GSM984398
Status Public on Oct 02, 2012
Title C42B H3K4ME3 treated
Sample type SRA
 
Source name prostate cancer cells
Organism Homo sapiens
Characteristics cell line: C4-2B
chip antibody: H3K4Me3
chip antibody manufacturer: Millipore
chip antibody lot #: DAM1661080
chip antibody catalog #: 07-473
treatment: DHT treated (4h)
Treatment protocol Cells were cultured in phenol red-free RPMI 1640 supplemented with 5% charcoal/dextran-stripped FBS (CSS) for 3 days. Cells were then treated with EtOH vehicle or 10nM DHT for additional 4 hr or 16 hr. For siRNA experiments cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 2 days, and then transfected with siRNA duplexes as indicated at a final concentration of 15nM using Lipofectamine RNAiMAX Transfection Reagent according to the manufacturer’s instructions. After transfection, cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 48 hr and then treated with 10nM DHT or vehicle for additional 16 hr.
Growth protocol Cells were maintained in RPMI 1640 medium with 5% fetal bovine serum (FBS).
Extracted molecule genomic DNA
Extraction protocol The ChIP-seq library was prepared according to the Illumina Protocol (www. illumina.com). Briefly, 10ng of ChIP DNA was end-repaired, ligated to barcoded adaptors, size selected on agrose gel (300-500 bp) and PCR amplified for 16 cycles using Phusion polymerase (Finnzymes). Ligation of 4 base adapters resulted in fragments consisting of the 4 base barcode followed by the sequence. The libraries were sequenced in the Illumina HiSeq2000 or Genome Analyzer IIx system according to the manufacturer’s instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description genomic DNA
Data processing bedgraph file: Samples were split according to barcode and barcodes were removed from fastq files. ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1. Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_H3K4ME3_TREATED.384.s_1.TCAT.bedGraph: hg18
 
Submission date Aug 10, 2012
Last update date May 15, 2019
Contact name Keith F Decker
E-mail(s) kfd1@cec.wustl.edu
URL http://pharmacogenomics.dom.wustl.edu/
Organization name Washington University School of Medicine
Department Internal Medicine
Lab Li Jia
Street address 660 S. Euclid Ave, Campus Box 8220
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL10999
Series (1)
GSE40050 Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions
Relations
SRA SRX176066
BioSample SAMN01112622

Supplementary file Size Download File type/resource
GSM984398_CHIPSEQ.C42B_H3K4ME3_TREATED.384.s_1.TCAT.bedGraph.gz 303.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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