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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 13, 2013 |
| Title |
Mouse_ERG_ERG_IP |
| Sample type |
SRA |
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| Source name |
Mouse Prostate
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: R26-ERG/ERG
chip antibody: Rabbit Anti-ERG (Epitomics Clone EPR3864)
age: 6 months
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| Growth protocol |
Mouse of each genotype was fed adlib. Prostate was isolated at 6 months of age
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| 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 R26-ERG/ERG prostates.
Genome_build: mm9
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks
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| Submission date |
May 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
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| Phone |
646-888-3356
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Human Oncology and Pathogenesis Program
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| Lab |
Chen
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| Street address |
1275 York Ave, Box 20
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL11002 |
| 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 |
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| Relations |
| BioSample |
SAMN02147267 |
| SRA |
SRX283735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1145303_Mouse_ERG_ERG_peaks.bed.gz |
205.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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