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Sample GSM1145670 Query DataSets for GSM1145670
Status Public on Jan 06, 2014
Title H2AZ_WT11_ZT06
Sample type SRA
 
Source name H2AZ_WT11_ZT06
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
antibodies: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001
Treatment protocol Mouse were exposed to a 12h light: 12h dark cycle (LD12:12) for at least 2 weeks before the experiment
Extracted molecule genomic DNA
Extraction protocol Adult mouse liver were collected at 6 different time of the day (mouse held under LD12:12, time points every 4hrs starting at ZT2)
Mouse liver were crosslinked with 1% formaldehyde for 10min, and nuclei were purified using standard sucrose cushion protocol.
Nuclei were resuspended, flash frozen in liquid nitrogen and stored at -80C.
Nuclei were thawed on ice, pelleted down and chromatin was digested with micrococcal nuclease.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
Following chromatin digestion with Mnase, H2AZ-containing nucleosome were imunoprecipitated using an anti-H2AZ antibody.
Immunoprecipitated chromatin (mononucleosome fraction) was purified and used for generating illumina libraries
Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA v1.7
Reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Uniquely mapped reads (51nt) were extended to 147nt to represent a full mononucleosome
H2AZ ChIP-Seq signal (MNase signal) was retrieved at genomic location of interest, and further normalized to sequencing depth
Genome_build: mm9
Supplementary_files_format_and_content: Table_GEO_H2AZsignal_at_CB3217peaks.txt contains average H2AZ ChIPseq signal at CLK:BMAL1 DNA binding sites; peak location of CLK:BMAL1 binding sites are in the file Table_GEO_CB3217_GenomicLocation_AllPeaks.txt
 
Submission date May 21, 2013
Last update date May 15, 2019
Contact name Jerome S Menet
E-mail(s) menet@bio.tamu.edu
Organization name Texas A&M University
Department Dept of Biology
Street address 301 Old Main Drive, Building 1530, ILSB
City College Station
State/province TX
ZIP/Postal code 77843
Country USA
 
Platform ID GPL13112
Series (2)
GSE47143 CLK:BMAL1 is a pioneer-like transcription factor [H2AZ-ChIP]
GSE47145 CLK:BMAL1 is a pioneer-like transcription factor
Relations
BioSample SAMN02152499
SRA SRX285101

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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