GEO DataSets

(Submitter supplied) Two decades after the introduction of oil-based vaccines in the control of bacterial and viral diseases in farmed salmonids, the mechanisms of induced side effects manifested as intra-abdominal granulomas remain unresolved. Side effects have been associated with generation of auto-antibodies and autoimmunity but underlying profile of the inflammatory and immune response has not been characterized. This study was undertaken with the aim to elucidate the inflammatory and immune mechanisms of granuloma formation at gene expression level associated with high and low side effect (granuloma) indices. Groups of Atlantic salmon parr were injected intraperitoneally with oil-adjuvanted vaccines containing either high or low concentrations of Aeromonas salmonicida or Moritella viscose antigens in order to induce polarized (severe and mild) granulomatous reactions. The established granulomatous reactions were confirmed by gross and histological methods at 3 months post vaccination when responses were known to have matured. The corresponding gene expression patterns in the head kidneys were profiled using salmonid cDNA microarrays followed by validation by real-time quantitative PCR (qPCR). qPCR was also used to examine the expression of additional genes known to be important in the adaptive immune response. Granulomatous lesions were observed in all vaccinated fish. Presence of severe granulomas were associated with a profile of up-regulation of innate immunity-related genes such as complement factors C1q and C6, mannose binding protein, lysozyme C, C-type lectin receptor, CD209, Cathepsin D, CD63, LECT-2, CC chemokine and metallothionein. In addition, IL-17A (Th17) was significantly up-regulated (p=0.009) in the group with severe granulomas as were arginase and IgM. None of the genes directly reflective of Th1 T cell lineage (IFN-γ, CD4) or Th2 (GATA-3) differentiation were differentially expressed. Granulomatous reactions following vaccination with oil-based vaccines in Atlantic salmon has the profile of strong expression of genes related to innate immune responses. The expression of IL-17A suggests an involvement of Th17 T cell lineage and is in conformity with strong infiltration of neutrophils and macrophages into inflamed areas. Arginase upregulation shows that macrophages in these reactions are alternatively activated, indicating a Th2-bias. To what extent the IL-17A profile reflects an autoimmune vaccine-based reaction remains elusive but would be in conformity with previous observations of autoimmune reactions in salmon vaccinated with oil-based vaccines.

Organism:

Oncorhynchus mykiss; Salmo salar; Oncorhynchus tshawytscha; Osmerus mordax; Coregonus clupeaformis

Type:

Expression profiling by array

Platform:

GPL2716

18 Samples

Download data: TXT

(Submitter supplied) Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify Atlantic salmon genes responsive to R. salmoninarum pathogen, fish were intraperitoneally injected with R. salmoninarum (BKD) or sterile KDM-2 medium (control). Head kidney samples were collected at 13 days post-infection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to different levels of R. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL11299

15 Samples

Download data: TXT

(Submitter supplied) Vaccination of pre-smolt salmon with a plasmid encoding the structural polypeptide of salmonid alphavirus subtype 3 (SAV3) gives protection against infection and development of pancreas disease (PD) mediated with production of antibodies against the virus. The present study analysed transcript responses in the muscle to vaccination with this plasmid (pSAV), pcDNA3.3 was used as a control. pSAV and pcDNA3.3 had similar abilities to up-regulate typical type I IFN stimulated genes. more...

Organism:

Salmo salar; Oncorhynchus mykiss

Type:

Expression profiling by array

Platform:

GPL16555

16 Samples

Download data: TXT

(Submitter supplied) A study was conducted to determine if different levels of vegetable and fish oils can alter antiviral responses of salmon macrophage-like cells (MLCs). Atlantic salmon were fed diets containing 7.38% (FO7) or 5.09% (FO5) fish oil. These diets were designed to be relatively low in EPA+DHA (i.e. FO7: 1.41% and FO5: 1%), but near the requirement level, resulting in no significant change in salmon growth. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL11299

24 Samples

Download data: TXT

(Submitter supplied) The study searched for the correlates of vaccine protection against furunculosis. After pathogen challenge of vaccinated (V) and unvaccinated (N) fish, hepatic gene expression was compared in salmon with high resistance (HR, individual samples) and low resistance (LR, pooled samples)

Organism:

Oncorhynchus mykiss; Salmo salar

Type:

Expression profiling by array

Platform:

GPL6154

11 Samples

Download data: GPR

(Submitter supplied) Infectious diseases among fish present an important economic burden for the aquaculture and fisheries industries around the world. For example, the infectious salmon anemia virus (ISAV) is known to infect farmed Atlantic salmon (Salmo salar), and results in millions of dollars of lost revenue to salmon farmers. Although improved management and husbandry practices over the last few years have minimized the losses and the number of outbreaks, the risk of new virulent isolates emerging is still a looming threat to the viability and sustainability of this industry. more...

Organism:

Oncorhynchus mykiss; Salmo salar

Type:

Expression profiling by array

Platform:

GPL8904

81 Samples

Download data: GPR

(Submitter supplied) After a 14-week feeding trial, Atlantic salmon fed a diet based on animal by-product meal and vegetable oil (ABP) showed lower growth rates compared to others fed an FM/FO-based diet (MAR). Interestingly, feeding a vegetable meal/oil-based diet (VEG) resulted in growth rates similar to the FM/FO-based diet. A 44K microarray experiment conducted on liver total RNA samples from these three dietary groups identified 46 genes related to metabolic and growth-relevant pathways, 25 immune-related, and 12 related to oxidation-reduction processes.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL11299

24 Samples

Download data: TXT

(Submitter supplied) Black spots, which deteriorate quality of Atlantic salmon fillets represent a significant problem for commercial aquaculture. These areas are characterized with accumulation of melanomacrophages, occasional formation of granulomas and substitution of skeletal muscle with connective tissue. Transcriptome analysis was performed to elucidate the origin and the character of inflammation in the melanized foci of skeletal muscle.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL30031

12 Samples

Download data: GPR

(Submitter supplied) Aeromonas salmonicida is a fish pathogen that causes furunculosis. Virulent strains of this bacterium are able to infect salmonid macrophages and survive within them, although mechanisms favouring intracellular survival are not completely understood. It is known that A. salmonicida cultured in vivo in the peritoneal cavity of the host undergoes changes in gene expression and surface architecture compared with cultures grown in vitro in broth. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL2844

24 Samples

Download data: TXT

(Submitter supplied) Infectious pancreatic necrosis (IPN) is widespread disease with global distribution and highly contagious, which leads to severe economic problems both freshwater and saltwater, particularly in the Atlantic salmon (Salmo salar). In this work we analyzed and evaluated gene expression profiles in resistant and susceptible families associated to S. salar exposed to IPNV in order to understand the defense mechanisms mounted by resistant fish in combating infection. more...

Organism:

Oncorhynchus mykiss; Salmo salar

Type:

Expression profiling by array

Platform:

GPL10679

8 Samples

Download data: TXT

(Submitter supplied) To study the short term (48 h) hepatic transcriptional changes and identify potential modes of action, Atlantic salmon (Salmo salar) were exposed to 15 mGy, 70 mGy and 280 mGy external gamma radiation. A combination of high density (60 k) custom oligonucleotide salmonid microarray and quantitative real-time reverse transcription polymerase chain reaction (qPCR) was employed to perform gene expression analyses. more...

Organism:

Salmo salar; salmonid fish

Type:

Expression profiling by array

Platform:

GPL18864

16 Samples

Download data: TXT

(Submitter supplied) Following an infection with a specific pathogen, the acquired immune system of many teleostean fish, including salmonids, is known to retain a specific memory of the infectious agent, which protects the host against subsequent infections. For example Atlantic salmon (Salmo salar), which have survived an infection with a low-virulence infectious salmon anemia virus (ISAV) isolate are less susceptible against subsequent infections with high-virulence ISAV isolates. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL7303

95 Samples

Download data: GPR

(Submitter supplied) This study investigates host-specific gene expression of the Pacific salmon lice, Lepeophtheirus salmonis oncorhynchii, while parasitizing a resistant host (Coho salmon), two susceptible hosts (Atlantic salmon, Sockeye salmon), and a population with-held hosts (starved), over 48 hrs.

Organism:

Lepeophtheirus salmonis

Type:

Expression profiling by array

Platform:

GPL15566

84 Samples

Download data: TXT

(Submitter supplied) In the present study a 44k oligonucleotide salmonid microarray, qPCR and histology were used to investigate transcriptomic responses in the distal intestine during the first week of oral exposure to soybean meal in order to gain insight into early molecular response mechanisms. Intestinal tissue samples were taken on day one, two, three, five and seven after introduction of a soybean-containing diet and compared to a control group fed fishmeal.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL11299

60 Samples

Download data: TXT

(Submitter supplied) MicroPoly(A)Pure kits (Ambion) were used to prepare mRNA from P. salmonis-infected and control Atlantic salmon head kidney. Head kidney mRNA samples were prepared from pooled (n = 10) infected or control kidney. Approximately 200 ng of infected or control head kidney mRNA was used as template in aRNA synthesis reactions. Two infected head kidney samples were pooled to yield 8.9 ug of aRNA, and a single control head kidney sample contained 8.4 ug of aRNA. more...

Organism:

Oncorhynchus mykiss; Salmo salar

Type:

Expression profiling by array

Platform:

GPL966

4 Samples

Download data: TIFF

(Submitter supplied) MicroPoly(A)Pure kits (Ambion) were used to prepare mRNA from P. salmonis-infected and control Atlantic salmon macrophages. Infected and control (24 h incubation) macrophage mRNA samples were subjected to two rounds of amplification using the MessageAmp aRNA kit (Ambion) and manufacturer's instructions. Approximately 400 ng of macrophage mRNA was used as template in the first round of amplification, yielding 8.1 ug of infected macrophage aRNA and 7.8 ug of control macrophage aRNA. more...

Organism:

Oncorhynchus mykiss; Salmo salar

Type:

Expression profiling by array

Platform:

GPL966

3 Samples

Download data: TIFF

(Submitter supplied) GRASP ~3600 gene salmonid cDNA microarray Keywords = Atlantic salmon Keywords = rainbow trout Keywords = salmonid

Organism:

Oncorhynchus mykiss; Salmo salar

4 Series

40 Samples

Download data

(Submitter supplied) Moritella viscosa is a bacterial pathogen causing winter-ulcer disease in Atlantic salmon. The lesions on affected fish lead to increased mortality, decreased fish welfare, and inferior meat quality in farmed salmon. MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation by guiding the miRNA induced silencing complex to specific mRNA transcripts (target genes). The goal of this study was to identify miRNAs responding to Moritella viscosa in salmon by investigating miRNA expression in head-kidney and the muscle/skin from lesion sites caused by the pathogen. more...

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL28080

23 Samples

Download data: TXT

(Submitter supplied) The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. more...

Organism:

Salmo salar

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24981

4 Samples

Download data: MTX, TSV

(Submitter supplied) Considerable interest and controversy has arisen over the potential effects of seismic surveys carried out during exploration for oil and gas deposits. Regarding fish, there is a concern that intense sound sources, such as seismic airguns, may injure their auditory system. In this study, salmonid cDNA microarrays and quantitative reverse transcription – polymerase chain reaction (QPCR) were used to identify and study a responsive gene set in the inner ear of Atlantic salmon (Salmo salar) following seismic airgun exposure. more...

Organism:

Oncorhynchus mykiss; Oncorhynchus tshawytscha; Osmerus mordax; Salmo salar; Coregonus clupeaformis

Type:

Expression profiling by array

Platform:

GPL10770

4 Samples

Download data: TXT