D differentially expressed genes in the skin of chum salmon at 6 days post exposure involved in immunity, proliferation, and other functions. Antiviral genes are suppressed as is seen in the anteriorSutherland et al. BMC Genomics 2014, 15:200 http://www.biomedcentral.com/1471-2164/15/Page 15 ofkidney of both Pacific salmon. Colors and formats are as described in Additional file 6: Figure S3. Addit
Sion analysis. Here all species were normalized together, and probes used only if they passed quality control in all species (Agilent). Enrichment analysis of up- or down-regulated gene lists was performed using Entrez-ID identifiers imported into the DAVID bioinformatics platform [78] using a background list specific to each species (all entities passing quality control filter for each experiment
T direction of fold change. Primers were designed to ensure equal amplification for all species to ensure correct estimates of expression levels, as shown for collagenase-3 log2(qPCR) against log2 (microarray) shown for (B) Atlantic and (C) pink salmon. chm = chum; pnk = pink; atl = Atlantic; AK = anterior kidney; S = skin; gene acronyms are as per the primer table (Additional file 4: Table S2). A
T direction of fold change. Primers were designed to ensure equal amplification for all species to ensure correct estimates of expression levels, as shown for collagenase-3 log2(qPCR) against log2 (microarray) shown for (B) Atlantic and (C) pink salmon. chm = chum; pnk = pink; atl = Atlantic; AK = anterior kidney; S = skin; gene acronyms are as per the primer table (Additional file 4: Table S2). A
D differentially expressed genes in the skin of chum salmon at 6 days post exposure involved in immunity, proliferation, and other functions. Antiviral genes are suppressed as is seen in the anteriorSutherland et al. BMC Genomics 2014, 15:200 http://www.biomedcentral.com/1471-2164/15/Page 15 ofkidney of both Pacific salmon. Colors and formats are as described in Additional file 6: Figure S3. Addit
Cal replicates were found to be within 0.5 Ct for all samples. The interplate calibrator used to compare across plates within a gene had a
Irus salmonis secretory/excretory products and their effects on Atlantic salmon immune gene regulation. Parasite Immunol 2007, 29(4):179?89. Fast MD, Muise DM, Easy RE, Ross NW, Johnson SC: The effects of Lepeophtheirus salmonis infections on the stress response and immunological status of Atlantic salmon (Salmo salar). Fish Shellfish Immunol 2006, 21(3):228?41. Fast MD, Ross NW, Johnson SC: Prost
Irus salmonis secretory/excretory products and their effects on Atlantic salmon immune gene regulation. Parasite Immunol 2007, 29(4):179?89. Fast MD, Muise DM, Easy RE, Ross NW, Johnson SC: The effects of Lepeophtheirus salmonis infections on the stress response and immunological status of Atlantic salmon (Salmo salar). Fish Shellfish Immunol 2006, 21(3):228?41. Fast MD, Ross NW, Johnson SC: Prost