|
| Status |
Public on May 12, 2015 |
| Title |
ZF-4 cells: MOCK vs NNV infected |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
NNV infected
|
| Organism |
Danio rerio |
| Characteristics |
cell line: ZF-4
time point: 6 hpi
|
| Treatment protocol |
ZF-4 cells were seeded in 12 well plates, and were inoculated with NNV. Cells were incubated with NNV at different 5 MOI for 1 hour. The cells were then wash to remove the unbound viral particles and further cultured at 28℃ then collected at 6 hpi.
|
| Growth protocol |
Cells were grown at 28℃ in RPMI 1640 medium (containing RPMI1640 powder, 10% FBS, 2g sodium bicarbonate, 10ml P/S, 10ml sodium pyruvate and 10ml L-G).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Agilent's Quick Amp Labeling Kit denerates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.
|
| |
|
| Channel 2 |
| Source name |
MOCK
|
| Organism |
Danio rerio |
| Characteristics |
cell line: ZF-4
time point: 6 hpi
|
| Treatment protocol |
ZF-4 cells were seeded in 12 well plates, and were inoculated with NNV. Cells were incubated with NNV at different 5 MOI for 1 hour. The cells were then wash to remove the unbound viral particles and further cultured at 28℃ then collected at 6 hpi.
|
| Growth protocol |
Cells were grown at 28℃ in RPMI 1640 medium (containing RPMI1640 powder, 10% FBS, 2g sodium bicarbonate, 10ml P/S, 10ml sodium pyruvate and 10ml L-G).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Agilent's Quick Amp Labeling Kit denerates fluorescent cRNA with a sample input RNA 1 μg of total RNA for two-color processing.The method uses T7 RNA polymerase,which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction (FE) Software (version10.5.1.1).
|
| Data processing |
Agilent Feature Extraction Software (v10.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
May 13, 2014 |
| Last update date |
May 12, 2015 |
| Contact name |
gen hwa lin |
| E-mail(s) |
genhwa@gate.sinica.edu.tw
|
| Phone |
886-2-27899534
|
| Organization name |
Academia Sinica
|
| Department |
Institute of Cellular and Organismic Biology
|
| Lab |
Lab of Marine Molecular Biology and Biotechnology
|
| Street address |
128,section2,academia road
|
| City |
Taipei |
| State/province |
Nankang |
| ZIP/Postal code |
11529 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6457 |
| Series (1) |
| GSE57600 |
Gene expression profile in NNV infected ZF-4 cells |
|
