|
| Status |
Public on Oct 01, 2015 |
| Title |
Hi-Myc_Castrate_AR_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Prostate, Castration 3 days prior
|
| Organism |
Mus musculus |
| Characteristics |
strain: Hi-Myc
tissue type: prostate tumor
ip antibody: AR IP (Epitomics clone ER179(2))
|
| Treatment protocol |
Mice underwent surgical castration or drug treat via oral gavage
|
| Growth protocol |
Hi-Myc transgenic mice were fed ad lib
|
| 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 |
ChIP-seq reads were obtained and mapped to the human genome (mm9 or build 37) using Bowtie to generate BAM files
Duplicates were removed using Samtools
Peak detection was performed with the software MACS (Version 1.4.1) with input as controls.
Genome_build: Build 37 or mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks
|
| |
|
| Submission date |
Oct 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| 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) |
| GSE62472 |
Cell context specific effect of AR antagonists on AR DNA binding and target gene expression |
| GSE62645 |
Effect of castration, bicalutamide, and enzalutamide on androgen receptor binding in Hi-Myc mouse prostate tumors |
|
| Relations |
| BioSample |
SAMN03140181 |
| SRA |
SRX739215 |
