|
| Status |
Public on Jan 31, 2012 |
| Title |
PPARalpha ChIP WT Control |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6 wild type mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: female
genotype/variation: wild type
treatment: Control
tissue: liver
ChIP: PPARalpha
antibody catalog #: SC-9000
antibody vendor/provider: Santa Cruz
|
| Treatment protocol |
Female C57BL/6 wild-type and LXRα/β-deficient mice (13 weeks of age) were treated by oral gavage once daily for 14 days with the RXR agonist bexarotene (100 mg/kg body weight [mpk], in 1% carboxymethylcellulose), the LXR agonist T0901317 (T09, 30 mpk) or vehicle alone.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was prepared from snap frozen livers, homogenized in PBS and cross-linked in 1% formaldehyde (10 min, RT). Cross-linked material was added 1M glycine to a final concentration of 0.125 M and incubated for 10 min rotating at RT, pelleted by centrifugation at 400xg for 2 min at 4°C, washed 2x in cold PBS and resuspended in lysis buffer (1% triton, 0.1% SDS, 150 mM NaCl, 2 mM EDTA, 1 mM EGTA, 20 mM Tris, pH 8.0) (200 μl/10 mg chromatin) before sonication according to the manufacturer’s protocol using the Diagenode Bioruptor twin (2x20 cycles, 30 sec. on/off, max. level). Samples were centrifuged for 2 min at 10.000xg and supernatant used for subsequent chromatin IP performed according to standard protocol. ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Read were mapped to mm9 using ELAND using 0 or 1 mismatches. Non-unique reads were discarded, ie only one read per genomic position was kept. The mapped reads were normalized between samples by uniformly removing reads to obtain an identical number of mapped reads for each experiment. Peaks were called using FindPeaks 4 with the parameters -subpeaks 0.1 and -trim-peaks 0.3. All peaks with less than 10 overlapping reads were discarded.
Genome Build:
PPARa_WT.bed: mm9
PPARa_WT_peaks.bed: mm9
|
| |
|
| Submission date |
Jan 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
|
| Phone |
+45 6550 2340
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE35262 |
Genome-wide profiling of LXR, RXR and PPARα in mouse liver reveals extensive sharing of binding sites |
|
| Relations |
| SRA |
SRX118173 |
| BioSample |
SAMN00779750 |
