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Sample GSM1145654 Query DataSets for GSM1145654
Status Public on Jan 06, 2014
Title Mnase_BM8_ZT10
Sample type SRA
Source name Mnase_BM8_ZT10
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
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 used for micrococcal nuclease diggestion.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
DNA was extracted (size ~150nt) and about 50ng of purified DNA was used for generating Illumina libraries
Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2000
Description Mnase-digested chromatin
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
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_MNase_signal_at_CB3217peaks_ALL.txt contains average nucleosome 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
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)
GSE47142 CLK:BMAL1 is a pioneer-like transcription factor [MNase-Seq]
GSE47145 CLK:BMAL1 is a pioneer-like transcription factor
BioSample SAMN02152479
SRA SRX285081

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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