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Sample GSM840528 Query DataSets for GSM840528
Status Public on Mar 29, 2012
Title REV-ERB alpha
Sample type SRA
 
Source name liver_REV-ERB alpha_ChIP
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
age: 20 wk
time point: ZT8
tissue: liver
chip antibody: REV-ERB alpha
Treatment protocol harvest time protocol : Mice were entrained for 3 days on a 12 hour light/dark cycle before livers were harvested at ZT8.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 2 mM disuccinimidyl glutarate for 30 minutes, then with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested.
Standard Illumina DNA library construction
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description 4086_4
Data processing Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (July 2007; mm9, NCBI Build 37) using Bowtie. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection was performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
 
Submission date Nov 29, 2011
Last update date May 15, 2019
Contact name Ruth T Yu
Organization name Salk Institute
Department Gene Expression Lab
Lab Ronald Evans
Street address 10010 N Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL9250
Series (2)
GSE34019 Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [ChIP_seq]
GSE34020 Integral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function
Relations
SRA SRX109461
BioSample SAMN00760894

Supplementary file Size Download File type/resource
GSM840528_ReverbA_4086.ucsc.bedGraph.gz 52.3 Mb (ftp)(http) BEDGRAPH
GSM840528_ReverbA_4086_peaks.txt.gz 459.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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