|
| Status |
Public on Jun 21, 2012 |
| Title |
Rat hepatocellular carcinoma cell line C5F |
| Sample type |
RNA |
| |
|
| Source name |
Rat HCC C5F
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: F344
gender: male
age: 31 weeks
tissue: Liver tumor
|
| Treatment protocol |
This rat hepatocellular carcinoma cell line is established from F344 rat treated with N-nitrosomorpholine and diethylnitrosamine (Ogawa et al., International Journal of Cancer, Vol. 91, pages 797–802, 2001.).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA is extracted with ISOGEN according to the manufacturers instructions.
|
| Label |
Cy5
|
| Label protocol |
2 µg of total RNA was processed following GE Healthcare's CodeLink(TM) iExpress Expression Assay Reagent Kit protocol. Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample.
|
| |
|
| Hybridization protocol |
After the fragmentation of 10 µg cRNA incubated at 94 ˚C for 20 minutes, hybridization is performed in a temperature-controlled shaking incubator for 18–24 h at 37 ˚C. After the hybridization, the slide is washed with 0.75× TNT in the bioarray rack at 46 °C for exactly 1 hr, and incubated in Cy5-Streptavidin working solution for 30 min at room temperature. The slide is washed four times with 1× TNT (5 minutes each wash), and rinsed in 0.1× SSC/0.05% TweenTM for 30 seconds. The slide is dried up with centrifuge.
|
| Scan protocol |
The slide is scanned with ArrayWoRx Biochip Reader using manufacturer recommended settings.
|
| Data processing |
The resulting images were processed through the CodeLink Expression Analysis v4.1 software which automatically grids and quantifies each feature while assigning spot quality metrics.
Data processing Raw values represent the final number of the spot after background is subtracted out. Normalized values represent median global normalization method, i.e. raw intensity/median intensity of all spots on the array.
|
| |
|
| Submission date |
Jul 07, 2011 |
| Last update date |
Jun 21, 2012 |
| Contact name |
Kumiko Ogawa |
| E-mail(s) |
ogawa93@nihs.go.jp
|
| Phone |
+81-3-3700-9818
|
| Fax |
+81-3-3700-1425
|
| Organization name |
National Institute of Health Sciences
|
| Department |
Pathology
|
| Street address |
1-18-1
|
| City |
Kamiyoga, Setagaya-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
158-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL2896 |
| Series (1) |
| GSE30469 |
comparison of mRNA expression among rat hepatoma cell lines with different metastatic ability |
|
