|
| Status |
Public on Jan 01, 2009 |
| Title |
GBM DNA hypermethylome: TSA vs mock in D54MG |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mock treated D54MG cells
|
| Organism |
Homo sapiens |
| Characteristics |
D54MG human GBM cell line
|
| Biomaterial provider |
Dr. Greg Riggins, Johns Hopkins Oncology Center
|
| Treatment protocol |
1x PBS for 96 hours
|
| Growth protocol |
McCoy's 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
|
| |
|
| Channel 2 |
| Source name |
TSA treated D54MG cells
|
| Organism |
Homo sapiens |
| Characteristics |
D54MG human GBM cell line treated with TSA
|
| Biomaterial provider |
Dr. Greg Riggins, Johns Hopkins Oncology Center
|
| Treatment protocol |
300 nanomolar TSA for 18 hour
|
| Growth protocol |
McCoy's 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
|
| |
|
| |
| 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 |
Identification of the GBM DNA hypermethylome revealed by gene expression profiling: TSA vs mock in D54MG
|
| Data processing |
Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor
|
| |
|
| Submission date |
Apr 11, 2008 |
| Last update date |
Dec 22, 2008 |
| Contact name |
Leander Van Neste |
| Organization name |
Ghent University
|
| Department |
Molecular Biotechnology
|
| Lab |
Bioinformatics and Computational Genomics
|
| Street address |
Coupure Links 653
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE11233 |
The Cancer Genome Atlas (TCGA) Consortium Integrated DNA Methylation Analysis |
|
