Transcriptome profiling of the antiviral immune response in Atlantic cod macrophages

This study was conduct to identify the virus-responsive transcripts in Atlantic cod, using viral mimic, polyriboinosinic polyribocytidylic acid (pIC) 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,