|
| Status |
Public on Jul 24, 2011 |
| Title |
7S - pool (16.11) 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ovarian cancer sample 7S
|
| Organism |
Homo sapiens |
| Characteristics |
drug response status: chemosensitive
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen primary ovarian tumor samples using the TRIzol reagent (Invitrogen, Burlington, ON, Canada) and finally dissolved in RNase-free H2O. Total RNA (5-10 μg) was treated with DNase using the RNase-free DNase kit and RNeasy spin columns (Qiagen, Mississauga, ON). Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2-0.5 μg/μl. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
|
| Label |
Cy5
|
| Label protocol |
fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using a fluorescent linear amplification kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (Perkin- Elmer, Boston, MA), following the user's manual.
|
| |
|
| Channel 2 |
| Source name |
pool (16.11)
|
| Organism |
Homo sapiens |
| Characteristics |
reference: pool of samples
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen primary ovarian tumor samples using the TRIzol reagent (Invitrogen, Burlington, ON, Canada) and finally dissolved in RNase-free H2O. Total RNA (5-10 μg) was treated with DNase using the RNase-free DNase kit and RNeasy spin columns (Qiagen, Mississauga, ON). Total RNA treated with DNase was dissolved in RNase-free H2O to a final concentration of 0.2-0.5 μg/μl. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
fluorescently labeled cRNA targets were generated from 0.5 μg of total RNA in each reaction using a fluorescent linear amplification kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (Perkin- Elmer, Boston, MA), following the user's manual.
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing was performed using the in situ Hybridization Plus Kit (Agilent) and following the manufacturer's instructions.
|
| Scan protocol |
The arrays were scanned using a dual-laser DNA microarray scanner (Agilent)
|
| Description |
209735213
|
| Data processing |
The data were then extracted from images by the Feature Extraction software 6.1 (Agilent). The raw data were processed in Bioconductor in R software packages. Data was normalized using the LOWESS normalization method. Filtering was done by selecting expressions below a threshold (log 2 of 100) that are present in at least 25% of the arrayed samples.
|
| |
|
| Submission date |
Apr 20, 2011 |
| Last update date |
Jul 24, 2011 |
| Contact name |
Xuan Bich Trinh |
| E-mail(s) |
[email protected]
|
| Organization name |
TCRU St. Augustinus GZA hospitals
|
| Street address |
Oosterveldlaan 24
|
| City |
Antwerp |
| ZIP/Postal code |
2610 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL7264 |
| Series (1) |
| GSE28739 |
Gene expression patterns of chemoresistant and chemosensitive serous epithelial ovarian tumors with possible predictive value in response to initial chemotherapy |
|
