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SRX283753: GSM1145321: Mouse_WT_input_IP; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina Genome Analyzer IIx) run: 66.2M spots, 2.4G bases, 1.3Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: 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
show Abstracthide Abstract
Translocation of ETS transcription factors including ERG and ETV1 occur in half of all prostate cancers. We generated a mouse model of ERG ovexpression (Rosa26-ERG) which when crossed into prostate specific probasin-Cre, expressed ERG specifically in the prostate. We crossed Rosa26-ERG into Pten flox/flox allele to generate compound GEMM mouse. Here, we determined the genomic binding sites of ERG, AR, and the histone marks H3K4me1 and H3K4me3 that maps enhancers and promoters respectively in the prostates of these mice. Overall design: The prostate of four six month old mice of each genotype were pooled. The chromatin was isolated and ChIP-Seq performed.
Sample: Mouse_WT_input_IP
SAMN02147285 • SRS426946 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina Genome Analyzer IIx
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction 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.
Experiment attributes:
GEO Accession: GSM1145321
Links:
External link:
Runs: 1 run, 66.2M spots, 2.4G bases, 1.3Gb
Run# of Spots# of BasesSizePublished
SRR86353466,165,1452.4G1.3Gb2015-07-22

ID:
401106

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