|
| Status |
Public on Nov 09, 2012 |
| Title |
ChIP-Seq_Mouse_Liver_ZT8_CLK |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Liver
age: Adult (3-6months)
antibody: anti-CLK (Novus Biological; #NB100-126; lot B1)
time: ZT8
|
| 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 |
Formaldehyde cross-linked mouse liver nuclei were sonicated. Chromatin was immunoprecipitated with specific antibodies against CLK or BMAL1. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA v1.6
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Peaks were called using Macs with the following setting: –bw=80 –-gsize=1890000000 –-tsize=36 –-mfold=5
Genome_build: mm9
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_Processed_data_Table1.txt: table with all significant CLK and BMAL1 peaks, their genomic location and relevant information. [Linked as supplementary file on Series record.]
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_BMAL1peaks_Macs_Analysis.txt: Output file from Macs analysis for peak calling
Supplementary_files_format_and_content: ChIPSeq_Mouse_Liver_CLKpeaks_Macs_Analysis.txt: Output file from Macs analysis for peak calling
|
| |
|
| Submission date |
Mar 28, 2012 |
| 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 |
GPL9250 |
| Series (2) |
| GSE36874 |
Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [ChIP-seq] |
| GSE36916 |
Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation |
|
| Relations |
| SRA |
SRX131982 |
| BioSample |
SAMN00997716 |
