|
| Status |
Public on Nov 15, 2010 |
| Title |
TR4_HepG2_ChIP-seq_rep1a |
| Sample type |
SRA |
| |
|
| Source name |
hepatocellular carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
harvest date: 2008-08-29
chip antibody: rabbit anti TR4 (JD Engel lab)
|
| Growth protocol |
All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei 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 (3 to 5 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 |
| |
|
| Description |
Chromatin IP against TR4
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)
|
| |
|
| Submission date |
Oct 13, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip Cayting |
| E-mail(s) |
pcayting@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Snyder
|
| Street address |
1501 S California Ave
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE24685 |
Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes |
|
| Relations |
| SRA |
SRX028638 |
| BioSample |
SAMN00115800 |
