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Sample GSM1145308 Query DataSets for GSM1145308
Status Public on Jun 13, 2013
Title Mouse_PTEN-ERG_ERG_IP
Sample type SRA
 
Source name Mouse Prostate
Organism Mus musculus
Characteristics strain: C57BL/6
genotype: Pten-f/f;R26-ERG/ERG
chip antibody: Rabbit Anti-ERG (Epitomics Clone EPR3864)
age: 6 months
Growth protocol Mouse of each genotype was fed adlib. Prostate was isolated at 6 months of age
Extracted molecule genomic DNA
Extraction protocol Prostates were dissected and then minced in 1.5ml tube with fine scissors. They were crosslinked for 15-minutes in 1% parformaldehyde. After quenching with glycine, the cross-linked chromatin was dounced and then 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 HiSeq 2000
 
Data processing All reads from ChIP-Seq were aligned to the mouse genome (build 37, or mm9) 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 Pten-f/f;R26-ERG/ERG prostates.
Genome_build: mm9
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 GPL13112
Series (2)
GSE47119 Genomic mapping of ERG, AR, histone H3 monomethyl-K4, histone H3 trimethyl-K4 binding sites in mouse prostates in WT, ERG overexpression, Pten loss mouse prostates
GSE47220 ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss
Relations
BioSample SAMN02147272
SRA SRX283740

Supplementary file Size Download File type/resource
GSM1145308_Mouse_PTEN-ERG_ERG_peaks.bed.gz 193.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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