|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 06, 2014 |
Title |
Mnase_BM9_ZT14 |
Sample type |
SRA |
|
|
Source name |
Mnase_BM9_ZT14
|
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 |
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) |
GSE47142 |
CLK:BMAL1 is a pioneer-like transcription factor [MNase-Seq] |
GSE47145 |
CLK:BMAL1 is a pioneer-like transcription factor |
|
Relations |
BioSample |
SAMN02152485 |
SRA |
SRX285087 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
|
|
|
|
|