|
| Status |
Public on Aug 08, 2007 |
| Title |
5Aza_vs_mock |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
5Aza-treated HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
HCT116 human colorectal cancer cell line
|
| Biomaterial provider |
Bert Vogelstein
|
| Treatment protocol |
5 micromolar 5Aza for 96 hours
|
| Growth protocol |
McCoys 5A medium with 10% BCS and 1x P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
|
| Label |
Cy5
|
| Label protocol |
Agilent low RNA input linear amplification kit
|
| |
|
| Channel 2 |
| Source name |
mock-treated HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
HCT116 human colorectal cancer cell line
|
| Biomaterial provider |
Bert Vogelstein
|
| Treatment protocol |
1x PBS for 96 hours
|
| Growth protocol |
McCoys 5A medium with 10% BCS and 1x P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
|
| Label |
Cy3
|
| Label protocol |
Agilent low RNA input linear amplification kit
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)
|
| 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 |
log ratio of red signal to green signal was calculated after background subtraction and loess normalization as implemented in the Limma package from Bioconductor
|
| |
|
| Submission date |
May 02, 2006 |
| Last update date |
Aug 08, 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 (2) |
| GSE4763 |
Identity of the human cancer cell DNA hypermethylome revealed by gene expression profiling |
| GSE4809 |
A Stem Cell-Like Chromatin Pattern May Predispose Tumor Suppressor Genes to DNA Hypermethylation |
|
