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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 06, 2014 |
| Title |
Mnase_BM10_ZT18 |
| Sample type |
SRA |
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| Source name |
Mnase_BM10_ZT18
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
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| Treatment protocol |
Mouse were exposed to a 12h light: 12h dark cycle (LD12:12) for at least 2 weeks before the experiment
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| 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.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Mnase-digested chromatin
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| 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
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| Submission date |
May 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jerome S Menet |
| E-mail(s) |
menet@bio.tamu.edu
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| Organization name |
Texas A&M University
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| Department |
Dept of Biology
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| Street address |
301 Old Main Drive, Building 1530, ILSB
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| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN02152492 |
| SRA |
SRX285094 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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