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Sample GSM1145324 Query DataSets for GSM1145324
Status Public on Jun 13, 2013
Title LNCaP-shScr-AR ChIP
Sample type SRA
 
Source name LNCaP cells
Organism Homo sapiens
Characteristics cell type: prostate cancer
chip antibody: Rabbit Anti-AR (Epitomics Clone ER179)
treatment: Scrambled shRNA infection x3 days
Growth protocol LNCaP cells were grown in 10% FBS. For baseline ChIP-Seq (ETV1 and H3K4me1 ChIP), 100 million and 20 million cells were harvested respectively. For ETV1 and scrambled knockdown experiments, 25 million cells were infected with lentiviral shRNA at MOI~5 and cells were harvested 72 hours later.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with 5 ug of the indicated antibody, washed, eluted, reverse cross-linked, and purified.
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 18 cycles. DNA was purified using Ampure beads and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description LNCaP Cells infected with scrambled shRNA (25 million), AR ChIP-Seq
Data processing All reads (36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one
Peaks were called using MACS 1.4 comparing with input DNA of LNCaP cells
Genome_build: hg18
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks
 
Submission date May 20, 2013
Last update date May 15, 2019
Contact name Yu Chen
E-mail(s) cheny1@mskcc.org
Phone 646-888-2163
Organization name Memorial Sloan Kettering Cancer Center
Department Human Oncology and Pathogenesis Program
Lab Chen
Street address 1275 York Ave, Box 20
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL10999
Series (2)
GSE47120 Effect of ETV1 knockdown on genome wide AR binding in LNCaP Cells
GSE47220 ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss
Relations
BioSample SAMN02147288
SRA SRX283756

Supplementary file Size Download File type/resource
GSM1145324_LNCAP-MOCK-ARChIP_peaks.bed.gz 62.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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