|
| Status |
Public on Mar 23, 2011 |
| Title |
SR2_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against SREBP-2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
antibody: antibody to a region of the mouse SREBP-2 within its amino-terminal nuclear targeted domain
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin preparation for ChIP assays and ChIP Seq using mouse livers were performed as previously described (Bennett et al., 2008; Seo et al., 2009). To prepare chromatin for the ChIP-seq, after isolating the ChIP-enriched DNA, gene-specific enrichment for known SREBP-2 target promoters relative to IgG control chromatin was verified. 20 ng of ChIP enriched DNA or control DNA was sent to Ambry Genetics (Aliso Viejo, CA) for high throughput DNA sequencing. The samples were blunt ended and adapters were ligated to the ends, according to the library preparation protocol from Illumina. Then DNA fragments with 200 ± 5bp in length were selected for the construction of the ChIP-seq DNA library. After size selection, all the resulting ChIPed DNA fragments were amplified and sequenced simultaneously using Solexa/Illumina Genome Analyzer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against SREBP-2
|
| Data processing |
Alignment: Short reads of 39-bp were produced from Solexa/Illumina Genome Analyzer, and mapped to a reference genome by Ambry Genetics using ELAND, allowing one mismatch. Short sequence reads that mapped to simple and complex repeats or that were not unique by chance were removed from the analysis.
Peaks: We used GLITR (Tuteja et al., 2009) to determine where areas where there were significantly more enriched reads mapped in the ChIP sample than in the IgG.
|
| |
|
| Submission date |
Mar 22, 2011 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Jacob Biesinger |
| E-mail(s) |
jake.biesinger@gmail.com
|
| Phone |
949 231 7587
|
| Organization name |
University of California, Irvine
|
| Department |
Computer Science
|
| Lab |
Xiaohui Xie
|
| Street address |
4058 Donald Bren Hall, University of California Irvine
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE28082 |
Examination of hepatic SREBP-2 binding using ChIP-Seq |
| GSE28084 |
Genome-wide Localization of SREBP-2 in Hepatic Chromatin Predicts a Novel Role in Autophagy |
|
| Relations |
| BioSample |
SAMN02196908 |
