|
| Status |
Public on Dec 06, 2012 |
| Title |
H3K4me3_ZT14 |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me3 IP
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
tissue type: liver
chip antibody: H3K4me3
chiip antibody manufacturer: Abcam
chip antibody catalog number: ab8580
chip antibody lot/batch: 376637
|
| Treatment protocol |
They were then entrained with a 12h Light/12h dark light regimen with food access between ZT12 and ZT24 for 7 days (ZT0 is defined as the time when the lights are turned on and ZT12 as the time when lights are turned off). At each ZT02 and, as a biological replicate, ZT26, five mice were anesthetized with isoflurane and decapitated. The livers were perfused with 5 ml of PBS through the spleen and immediately collected. Up to 100 mg of liver was snap-frozen in liquid nitrogen and kept at -80°C for RNA extraction. The rest of the livers was immediately homogenized in PBS containing 1% formaldehyde for chromatin preparation.
|
| Growth protocol |
C57/BL6 male, 12-14 week old (at time of sacrifice), mice were housed in a 12h Light/12h dark light regimen for 2 weeks with food and water available ad libitum during night and day.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin from cell lysates was sonicated and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 |
Reads were mapped on the reference mouse genome NCBI37/mm9 using Bowtie allowing three mismatches and reporting up to five alignments on the genome. Duplicated reads were removed. The coverage per window size of 500 bases was calculated and a summary graph file with window size 500, in bedGraph format, is available for each sample. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/
Genome Build:
H3K4me3_ZT14.bedGraph: (NCBI37/mm9)
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nouria Hernandez |
| E-mail(s) |
nouria.hernandez@unil.ch
|
| Organization name |
UNIL
|
| Department |
CIG
|
| Lab |
Hernandez
|
| Street address |
Dorigny
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE35788 |
Genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle |
| GSE35790 |
Kinetic RNA polymerase II occupancy, associated histone marks, and mRNA accumulation reveal transcriptional and post-transcriptional mechanisms underlying circadian gene expression |
|
| Relations |
| SRA |
SRX119661 |
| BioSample |
SAMN00788795 |
