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| Status |
Public on Jan 06, 2014 |
| Title |
CLK_Input_Sonicated_WT30_ZT06 |
| Sample type |
SRA |
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| Source name |
CLK_Input_Sonicated_WT30_ZT06
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
antibodies: none, input
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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 chromatin either was digested with micrococcal nuclease or sonicated using Bioruptor.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
Following chromatin shearing, chromatin was imunoprecipitated using an anti-CLK antibody.
Immunoprecipitated chromatin and inpur 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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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
CLK ChIP-Seq signal was retrieved at genomic location of interest, and further normalized to sequencing depth
Genome_build: mm9
Supplementary_files_format_and_content: Table_GEO_CLK_ChIPseqSignal_MNase_vs_Sonication.txt contains average CLK 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
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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) |
| GSE47144 |
CLK:BMAL1 is a pioneer-like transcription factor [CLK_ChIP] |
| GSE47145 |
CLK:BMAL1 is a pioneer-like transcription factor |
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| Relations |
| SRA |
SRX285137 |
| BioSample |
SAMN02152473 |
| 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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