|
| Status |
Public on Aug 08, 2011 |
| Title |
Huh7 AR ChIP-chip Slide 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Huh7 cells immunoprecipitated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
antibody: anti-AR
vendor: Millipore/Upstate
catalogue #: 06-680
|
| Treatment protocol |
No treatment was performed. AR target genes in normal condition were identified.
|
| Growth protocol |
The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.
|
| Label |
Cy5
|
| Label protocol |
DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.
|
| |
|
| Channel 2 |
| Source name |
Huh7 cells input
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
|
| Treatment protocol |
No treatment was performed. AR target genes in normal condition were identified.
|
| Growth protocol |
The 2 HCC cell lines were maintained in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed as described previously (Lee et al. Nat Protoc 2006;1:729-748). IP and input DNA were then purified with standard phenol/chloroform method.
|
| Label |
Cy3
|
| Label protocol |
DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505B scanner.
|
| Description |
Agilent ChIP-on-chip set 1 of 2
|
| Data processing |
Agilent Feature Extraction Software (9.5.3.1) was used for background subtraction and LOWESS normalization log2 ratio (test/reference).
|
| |
|
| Submission date |
Dec 06, 2010 |
| Last update date |
Aug 08, 2011 |
| Contact name |
Hai Feng |
| E-mail(s) |
fogsea@163.com
|
| Phone |
852-37636104
|
| Fax |
852-21445330
|
| Organization name |
The Chinese University of Hong Kong
|
| Street address |
The Chinese University of Hong Kong
|
| City |
Hong Kong |
| ZIP/Postal code |
852 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL4125 |
| Series (1) |
| GSE25884 |
Delineation of AR oncogenic functions in hepatocellular carcinoma |
|
