 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 31, 2016 |
| Title |
Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages |
| Organism |
Gadus morhua |
| Experiment type |
Expression profiling by array
|
| Summary |
This study was conduct to identify the virus-responsive transcripts in Atlantic cod, using viral mimic, polyriboinosinic polyribocytidylic acid (pIC)
|
| |
|
| Overall design |
Six individual Atlantic cod (1.087 ± 0.73 kg) were used for identification of antiviral (i.e. pIC-responsive) macrophage transcripts. The fish were kept in a 21 m^3 tank and optimum conditions (5.2-6.4˚C, 95-110% oxygen saturation and under an ambient photoperiod) in the Dr. Joe Brown Aquatic Research Building (JBARB) of the Ocean Sciences Centre (OSC).
Atlantic cod head kidney cells were isolated from 6 fish. The cells were allowed to adhere overnight (16 h) at 10˚C, and then the non-adherent cells were removed. Thereafter, macrophages (adherent cells) from each individual were exposed to either viral mimic using 50 ug/ml pIC or PBS (control). Macrophages were lysed at 24 HPS using TRIzol, and RNAs were extracted. A common reference design was used for the microarray experiment. For each group (pIC or control), 6 biological replicates (pIC and control from 6 fish) were used for microarray experiment. The common reference consisted of a pool of 12 RNA samples. All test samples were labeled with Cy5, whereas common reference was labeled with Cy3. Each individual test sample was co-hybridized with the common reference sample on an array (20K Atlantic cod microarray platform); therefore, 12 arrays were used for this experiment.
[variable] other: pIC: Fish_1_pIC, Fish_2_pIC, Fish_3_pIC, Fish_4_pIC, Fish_5_pIC, Fish_6_pIC,
[variable] other: Control: Fish_1_Control, Fish_2_Control, Fish_3_Control, Fish_4_Control, Fish_5_Control, Fish_6_Control,
[repeat] biological replicate: Fish_1_pIC, Fish_2_pIC, Fish_3_pIC, Fish_4_pIC, Fish_5_pIC, Fish_6_pIC,
[repeat] biological replicate: Fish_1_Control, Fish_2_Control, Fish_3_Control, Fish_4_Control, Fish_5_Control, Fish_6_Control,
|
| |
|
| Contributor(s) |
Eslamloo K, Xue X, Booman M, Rise ML |
| Citation(s) |
27255218 |
| |
| Submission date |
Jul 12, 2015 |
| Last update date |
Nov 30, 2016 |
| Contact name |
Khalil Eslamloo |
| E-mail(s) |
keslamloo@mun.ca
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Ocean Sciences
|
| Lab |
Rise Lab
|
| Street address |
0 Marine Lab Rd.
|
| City |
St. John's |
| State/province |
Newfoundland and Labrador |
| ZIP/Postal code |
A1C 5S7 |
| Country |
Canada |
| |
|
| Platforms (1) |
| GPL10532 |
CGP Atlantic cod 20K oligo array v1.0 |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA289607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE70808_RAW.tar |
108.9 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...