|
| Status |
Public on Nov 25, 2013 |
| Title |
SMRT ChIPSeq 5AM (ZT22) |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
time: ZT22
strain: C57BL/6
chip antibody: SMRT
chip antibody manufacturer: Abcam
chip antibody catalog #: 24551
|
| Treatment protocol |
No treatment involved.
|
| Growth protocol |
Mice were fed ad libum and euthanized at 5 pm (ZT10) and 5 am (ZT22).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell lysates were prepared from cross-linked livers. After sonication, histone-DNA complexes were immunoprecipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Seq DNA Sample Prep Kit (Illumina IP-102-1001). 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 (32 to 52 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 ~250 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 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequencing and alignment: Sequencing was done by the Functional Genomics Core at the University of Pennsylvania. Sequence reads were processed and mapped to the mouse genome (mm8) using ELAND pipeline. Before subsequent analysis, edundant reads in each genomic position were condenced into one to avoid possible PCR bias or each sample.
Peak Calling: Peak calling was performed by Homer with default parameters then 1rpm cut-off was applied, where all the redundant reads per position were condensed into one.
Genome_build: mm8
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Sep 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hee-Woong Lim |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Biomedical Informatics
|
| Street address |
3333 Burnet Ave. MLC 7024
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE51045 |
Genome-wide mapping of SMRT (silencing mediator of retinoid and thyroid hormone receptors) occupancy in mouse liver at different Zeitgeber times (ZTs). |
|
| Relations |
| BioSample |
SAMN02360491 |
| SRA |
SRX357100 |
