GEO DataSets

(Submitter supplied) Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. more...

Organism:

Oncorhynchus mykiss

Type:

Other

Platform:

GPL30022

6 Samples

Download data: TXT

(Submitter supplied) Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29994

6 Samples

Download data: TXT

(Submitter supplied) Rainbow trout (Oncorhynchus mykiss) is one of the economically important cold-water fish cultivated in the world. The outbreak of infectious hematopoietic necrosis (IHN) seriously restricted the development of rainbow trout farming industry and caused huge economic losses. Fish skin is the largest mucosal immune organ, providing the first line of defense against pathogen invasion. However, the immune mechanisms associated with fish skin remain unclear. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23000 GPL29994

12 Samples

Download data: TXT

(Submitter supplied) Directional selection in the domestication of fish species has resulted in rapid gains of growth, body size, and other production-relevant traits in relatively few generations. While there is clear evidence of genetic divergence contributing to selection-related phenotypic changes, emerging research suggests that intergenerational epigenetic inheritance may also be a relevant mechanism explaining rapid evolutionary change in domestic fish lines. more...

Organism:

Salvelinus fontinalis

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL33246

40 Samples

Download data: BEDGRAPH

(Submitter supplied) The objective of this study was to identify metabolic regulatory mechanisms affected by choline availability in rainbow trout (Oncorhynchus mykiss) broodstock diets associated with increased offspring growth performance. Three customized diets were formulated to have different levels of choline: (a) 0% choline supplementation (Low Choline: 2065 ppm choline), (b) 0.6% choline supplementation (Medium Choline: 5657 ppm choline), and (c) 1.2% choline supplementation (High Choline: 9248 ppm choline). more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23004

36 Samples

Download data: XLSX

(Submitter supplied) Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29994

18 Samples

Download data: CSV

(Submitter supplied) Dissolved oxygen (DO) has an important impact on fish survival and reproduction, and is also one of the keys limiting conditions for healthy fish life. Rainbow trout (Oncorhynchus mykiss), an economically significant cold-water fish globally, are highly susceptible to hypoxia stress. However, the physiological changes and molecular mechanisms of rainbow trout under different hypoxic conditions are still unknown. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29994

9 Samples

Download data: TXT

(Submitter supplied) Comparison of two single cell transcriptomic approaches to investigate cellular heterogeneity within the head kidney of healthy farmed Atlantic salmon (Salmo salar)

Organism:

Salmo salar

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24981 GPL28848

4 Samples

Download data: MTX, TSV

(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) Rainbow trout (Oncorhynchus mykiss) is a well-known economical fish globally, and its market value and acceptance are greatly influenced by skin color. However, the molecular mechanisms underlying skin color variation in rainbow trout remains largely unknown. In this study, we compared the expression profiles of whole transcriptome in dorsal skin from wild-type (WTrt) and yellow mutant rainbow trout (YMrt) that are F1 generation of WTrt ♂ × YMrt ♀. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23000 GPL24430

12 Samples

Download data: TXT

(Submitter supplied) As part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. more...

Organism:

Oncorhynchus mykiss; Xenopus laevis; Coturnix japonica; Lithobates pipiens; Phalacrocorax auritus; Pimephales promelas

Type:

Expression profiling by high throughput sequencing

9 related Platforms

724 Samples

Download data: TXT

(Submitter supplied) The frequency of fish encountering hypoxia has risen dramatically as global warming and water pollution intensify, posing a serious threat to survival. Rainbow trout (Oncorhynchus mykiss), which is an economically important fish worldwide, belongs to a typical hypoxia-sensitive fish. However, little is known about the response mechanisms employed by rainbow trout to hypoxia stress. In this study, we systematically analyzed the changes of liver biochemical parameters in rainbow trout exposed to moderate hypoxic conditions (DO: 4.5 ± 0.1 mg/L) for different durations (4, 8, 12, 24 h and 1 month) and 12 h and 24 h reoxygenation, and histologic and transcriptome (lncRNA, miRNA and mRNA) under hypoxia stress for 12 h (Tm12L) and 1 month (TmlL) compared with control, and the interaction between LOC110520201, miR-2188-y and sod1 was verified by dual-luciferase reporter, overexpression and silencing assays. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24430 GPL23000

12 Samples

Download data: TXT

(Submitter supplied) The rainbow trout (Oncorhynchus mykiss) is one of the most important aquaculture species worlwide. In this study, transcriptional profiling of skin by oligonucleotide microarray was applied to rainbow trout individuals infected with A. salmonicida, to identified enriched genes involved in pathogen response.

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by array

Platform:

GPL16819

7 Samples

Download data: TXT

(Submitter supplied) Transcriptomics ananlysis of olfactory organs of Atlantic salmon. Controls/untreated (C) fish were compared to fish that were exposed to low (L) or high (H) concentrations of hydrogen sulphide.

Organism:

Salmo salar

Type:

Expression profiling by array

Platform:

GPL33906

36 Samples

Download data: TXT

(Submitter supplied) Rainbow trout (1000 fish) was exposed to the bacterial pathogen F. psychrophilum by simple bath challenge without any pre-treatment with hydrogen peroxide. Samples (fin clip for Affymetrix QTL analysis) were taken from 167 moribund fish during the course of infection. When mortality/morbidity ended (day 40) we euthanized a total of 197 specimens of the remaining fish and took samples for DNA (QTL analysis) and assigned the status: Survivor. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by RT-PCR

Platform:

GPL32679

270 Samples

Download data: XLSX

(Submitter supplied) Non-Saccharomyces yeast such as Debaryomyces hansenii or its cell wall-components are emerging candidates for novel functional aquafeeds, as they contain several microbe-associated molecular patterns (MAMPs) that can activate and modulate the host’s physiological responses and improve fish health and welfare. RNAseq results showed an upregulation in pathways associated with humoral immunity and complement activation in the liver. more...

Organism:

Salmo salar

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24981

48 Samples

Download data: TXT

(Submitter supplied) Production of sterile fishes through artificial retention of a third set of chromosomes (triploidy) is a sustainable alternative for aquaculture since it reduces pressure on wild populations. However, these fishes have reduced survival in stressful conditions and in response to pathogens. In this study, the impact of Vibrio anguillarum infection on diploid and triploid Chinook salmon (Oncorhynchus tshawytscha) was investigated to identify if there was any significant regulation by microRNAs (miRNA) in immune responsive tissues. more...

Organism:

Oncorhynchus tshawytscha

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32570

56 Samples

Download data: TAB

(Submitter supplied) Hypoxia is a tricky and unavoidable environmental stressor for aquaculture with ongoing ecological deterioration and increasing stocking density, resulting in serious economic losses. Rainbow trout (Oncorhynchus mykiss), a commercially important fish species worldwide, exhibits extraordinarily poor tolerance to hypoxia; however, the regulatory mechanisms under hypoxia stress have not been elucidated. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24430

9 Samples

Download data: TXT

(Submitter supplied) Hypoxia is a tricky and unavoidable environmental stressor for aquaculture with ongoing ecological deterioration and increasing stocking density, resulting in serious economic losses. Rainbow trout (Oncorhynchus mykiss), a commercially important fish species worldwide, exhibits extraordinarily poor tolerance to hypoxia; however, the regulatory mechanisms under hypoxia stress have not been elucidated. more...

Organism:

Oncorhynchus mykiss

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23000

9 Samples

Download data: TXT

(Submitter supplied) Hypoxia negatively affects the behavior, growth, reproduction, and survival of fish, causing serious economic losses to aquaculture. Rainbow trout (Oncorhynchus mykiss), an important economic fish worldwide, belongs to a hypoxia-sensitive fish species. However, the regulatory mechanisms of miRNAs under hypoxia stress response of rainbow trout remains unclear. In this study, rainbow trout were subjected to hypoxia stress (DO: 3.5 mg/L) for 3 h (H3h_L), 12 h (H12h_L), 24 h (H24h_L) and 3 h reoxygenation (R3h_L) to systemically evaluate the changes of miRNA expression profiles in liver, and the functions of sha-miR-92a_L+2R+4 were investigated. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23000

15 Samples

Download data: TXT