|
| Status |
Public on Apr 01, 2014 |
| Title |
RFKO_233 |
| Sample type |
SRA |
| |
|
| Source name |
RFKO_233
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57 BL/6
tissue type: liver
genotype/variation: hs-RXRa-del-exon4-/-
gender: female
antibody: RXRa (D-20)
antibody manufacturer: Santa Cruz Biotechnology
antibody catalog number: sc-553
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA were extracted from the cells and fragmented via nebulization. The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by Chip treatments of RxRa and Pol II respectively. Sizes between 200 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer II.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RFKO_233
|
| Data processing |
Reads are mapped to genome using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. MACS is used to call peaks with p value 1e-10.
|
| |
|
| Submission date |
May 05, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
|
| Phone |
(713) 677-7439
|
| Organization name |
Texas A&M University
|
| Street address |
2121 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE21696 |
Genome-wide analysis of RXRa binding in mouse liver chromatin with ChIP-SEQ. |
| GSE47899 |
Genome-wide analysis of liver in male and female mice |
|
| Relations |
| SRA |
SRX020169 |
| BioSample |
SAMN00012731 |
