|
| Status |
Public on Mar 10, 2014 |
| Title |
SREBP1 (ZT14) |
| Sample type |
SRA |
| |
|
| Source name |
SREBP1_ZT14, liver cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6
genotype/variation: wild type
gender: male
tissue: liver
time: ZT14
chip antibody: SREBP1
chiip antibody manufacturer: Santa Cruz Biotechnology
chip antibody catalog number: sc-8984x
chip antibody lot/batch: I0909
|
| 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.
Enriched peaks, in bedGraph format, are available for each sample.
Additional processed data and visualization tools are available at “http://cyclix.vital-it.ch”.
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files were generated after peaks definition. Scores represent nucleotide counts in the refined peaks normalized according to the total number of non redundant mapped reads
|
| |
|
| Submission date |
Jun 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Beatrice Desvergne |
| Organization name |
UNIL
|
| Department |
CIG
|
| Lab |
Desvergne
|
| Street address |
Dorigny
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE48375 |
Dynamics of SREBP1 binding to DNA in mouse liver |
|
| Relations |
| BioSample |
SAMN02216838 |
| SRA |
SRX316700 |
