|
| Status |
Public on Sep 27, 2014 |
| Title |
PPARα KO ChIP-seq_GW7647 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age and sex: 8-week-old
age sex: male
nutrient state: ad libitum fed
|
| Treatment protocol |
Vehicle (4:1 mixture of PEG-400 and Tween80), GW7647 (5 mg/kg body weight), twice, oral gavage at 12:00 am and 12:00 pm
|
| Growth protocol |
All mice maintained in ad libitum normal chow diet and drinking water
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Liver harvested from anesthetized mouse was snap-frozen in liquid nitrogen. Lysates were clarified from sonicated nuclei and PPARα-genomic DNA complexes were isolated with PPARα antibody.
10 ng of the pooled DNA was then amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GW7647 treatment (twice, oral gavage, 12:00 am and 12:00 pm)
|
| Data processing |
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters ‘-n 1 -l 30 -m 1’. Only one uniquely aligning read per genomic position was kept for further analysis.
Peakcalling and wiggle file generation was performed with MACS14 using default settings. Then normalized to the total number of reads for each sample (reads/per million reads)
Genome_build: mm9
|
| |
|
| Submission date |
Sep 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
David Moore |
| E-mail(s) |
moore@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN03082090 |
| SRA |
SRX711582 |
