|
| Status |
Public on Mar 21, 2012 |
| Title |
DAC Treated Kasumi CD34+ [mRNA profiling] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mock treated Kasumi-1 CD34+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 1XPBS for 72 hours
cell type: Leukemia Cell Line
cell line: Kasumi CD34+
|
| Treatment protocol |
10nM DAC for 72 hours
|
| Growth protocol |
McCoy's 5A medium with 10% BCS and 1x PBS
|
| 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 |
DAC treated Kasumi-1 CD34+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 10nM DAC
cell type: Leukemia Cell Line
cell line: Kasumi CD34+
|
| Treatment protocol |
10nM DAC for 72 hours
|
| Growth protocol |
McCoy's 5A medium with 10% BCS and 1x PBS
|
| 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 |
Samples were amplified and labeled using Quick Amp Labeling Kit (Cat# 5190-0447, Agilent Technologies), Full Spectrum Primers (Cat# RA300A-2, System Bioscience), Cynine-3-CTP and Cynine-5-CTP (Perkin Elmer), and hybridized using Gene Expression Hybridization Kit by following manufacturer's protocol (G4140-90050, Agilent Technologies)
|
| Scan protocol |
Microarrays were scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 5 micrometer resolutions. Data were extracted using Feature Extraction Software v9.5.3.1 (Agilent Technologies) and protocol for gene expression microarrays.
|
| Description |
Characterization of gene expression changes after treatment with the DNA methylation inhibitor DAC
|
| 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 |
Dec 06, 2011 |
| Last update date |
Mar 21, 2012 |
| 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 |
GPL6480 |
| Series (1) |
|
