GEO DataSets

(Submitter supplied) Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. more...

Organism:

Oncorhynchus mykiss; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29994 GPL24676

552 Samples

Download data: TXT

(Submitter supplied) Over the last century, rainbow trout (RBT) has been widely used as a biological model in many biological disciplines and has become one of the best-studied fish. For example, RBT is an excellent model to study gene evolution as it is a partially tetraploid organism that underwent a whole-genome duplication (salmonid-specific 4th WGD) followed by a partial re-diploidization and significant genome rearrangements. more...

Organism:

Oncorhynchus mykiss

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL24430

78 Samples

Download data: BED, BROADPEAK, COV

(Submitter supplied) In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters. Paradoxically, PRDM9 induces the self-destruction of its targets and this triggers an ultra-fast evolution of mammalian hotspots. more...

Organism:

Oncorhynchus mykiss

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29994

18 Samples

Download data: BED, BIGWIG, BW

(Submitter supplied) Single cell RNA-Seq data generated on a 10x Chromium genomics platform from infected and healthy PBLs from Oncorhynchus mykiss.

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23004

4 Samples

Download data: TAR

(Submitter supplied) A critical problem facing all U. S. aquaculture is loss due to disease. In the past year alone, diseases accounted for 90% of all losses of trout intended for sale, greatly impacting the livelihood of our farmers. Previously, we focused on sustainable aquaculture efforts by evaluating the effects of dietary replacement (marine-based to plant-based protein sources) on rainbow trout. Through this effort, we developed a rainbow trout strain that thrives on an all plant-protein formulated diet (PSel/UI strain). more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24430

270 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:

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:

GPL29994 GPL23000

12 Samples

Download data: TXT

(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) 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) 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) 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

(Submitter supplied) Gynogenetic development in fish is induced by activation of eggs with irradiated spermatozoa followed by exposure of the activated eggs to the temperature or high hydrostatic pressure (HHP) shock that prevents 1st cell cleavage. Produced specimens are fully homozygous fish also known as Doubled Haploids. Gynogenetic DH individuals might be used aquaculture and developmental biology unfortunately; the potential application of DHs is limited by a rather low survival rate of such specimens. more...

Organism:

Oncorhynchus mykiss

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29994

14 Samples

Download data: TXT