|
| Status |
Public on Oct 26, 2007 |
| Title |
TERA_ATRA_vs_mock_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ATRA-treated TERA2
|
| Organism |
Homo sapiens |
| Characteristics |
TERA2 human embryonal carcinoma cell line
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
2 micromolar all_trans retinoic acid for 12 days
|
| Growth protocol |
McCoy's 5A medium with 10% BCS and 1x P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction followed by RNeasy clean-up with on-column DNase treatment
|
| Label |
Cy3
|
| Label protocol |
Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol
|
| |
|
| Channel 2 |
| Source name |
Mock-treated TERA2
|
| Organism |
Homo sapiens |
| Characteristics |
TERA2 human embryonal carcinoma cell line
|
| Biomaterial provider |
ATCC
|
| Treatment protocol |
None
|
| Growth protocol |
McCoy's 5A medium with 10% BCS and 1x P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction followed by RNeasy clean-up with on-column DNase treatment
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit using manufecturer's recommended protocol
|
| Scan protocol |
Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays
|
| Description |
None
|
| Data processing |
log2 Ratio of background subtracted ATRA intensity to background subtracted Mock treated intensity after loess normalization with Bioconductor
|
| |
|
| Submission date |
May 11, 2006 |
| Last update date |
Apr 26, 2007 |
| Contact name |
Wayne Yu |
| E-mail(s) |
wyu8@jhmi.edu
|
| Phone |
(410)502-7970
|
| Fax |
(410)955-8780
|
| Organization name |
Johns Hopkins University
|
| Department |
Cancer Center
|
| Street address |
417 N. Caroline St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL1708 |
| Series (1) |
| GSE4809 |
A Stem Cell-Like Chromatin Pattern May Predispose Tumor Suppressor Genes to DNA Hypermethylation |
|
