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Sample GSM1586664 Query DataSets for GSM1586664
Status Public on Feb 12, 2016
Title AR_LNCaP_Mib_rep2
Sample type SRA
 
Source name AR_LNCaP_Mib
Organism Homo sapiens
Characteristics cell line: LNCaP
cell type: prostate cancer cell line
treated with: 10 nmol/l of mibolerone
chip antibody: AR (N-20)
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-816
Treatment protocol The cells were cultures with charcoal-stripped (steroid depleted) serum medium for 48 hours and then treated with ethanol or 10 nmol/l of mibolerone (BIOMOL, Plymouth Meeting, PA). For PSA eRNA knocking down, the cells were transfected with control siRNA or PSA si-eRNA for 48 hours and two roundly.
Growth protocol Prostate cancer cells were cultures (typically 2-3 × 10^6 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Pol2 differential binding was analyzed by edgeR(v3.6.8)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file
 
Submission date Jan 16, 2015
Last update date May 15, 2019
Contact name LIGUO WANG
E-mail(s) wang.liguo@mayo.edu
Organization name Mayo Clinic
Department Division of Computational Biology
Street address 200 1st St SW
City Rochester
State/province MN
ZIP/Postal code 55905
Country USA
 
Platform ID GPL11154
Series (2)
GSE55032 Activation of the P-TEFb Complex by Lethal Prostate Cancer-Associated Enhancer RNAs
GSE65066 Activation of P-TEFb by enhancer RNAs associated with lethal prostate cancer [ChIP-seq]
Relations
BioSample SAMN03287210
SRA SRX847034

Supplementary file Size Download File type/resource
GSM1586664_AR_LNCaP_Mib_rep2.bw 55.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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