GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32658

174 Samples

Download data

(Submitter supplied) To explore the effects of the housing condition (group- or single-housing) on killifish, we performed RNA-seq analysis for the whole bodies of male and female juveniles, gonads of males and females from puberty to middle age, and livers of young and old males.

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32658

86 Samples

Download data: TXT

(Submitter supplied) To explore the effects of the housing condition (group- or single-housing) on killifish, we performed RNA-seq analysis for the whole bodies of male and female juveniles, gonads of males and females from puberty to middle age, and livers of young and old males.

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32658

88 Samples

Download data: TXT

(Submitter supplied) This study elucidated the role of DHA-modulated genes in the development and growth of bluefin tuna (Thunnus thynnus) larvae ingesting increasing levels of DHA in their rotifer prey. The effect of feeding low, medium, and high rotifer (Brachionus rotundiformis) DHA levels (2.0, 3.6 and 10.9 mg DHA g-1 DW, respectively) was tested on 2-15 days post hatching (dph) bluefin tuna larvae. Larval DHA content markedly (P < 0.05) increased in a DHA dose-dependent manner (1.5, 3.9, 6.1 mg DHA g-1 DW larva, respectively), that was positively correlated with larval prey consumption, and growth (P < 0.05). more...

Organism:

Thunnus thynnus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34366

30 Samples

Download data: CSV, XLSX

(Submitter supplied) Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genomes revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. more...

Organism:

Syngnathus scovelli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34966

2 Samples

Download data: RDS

(Submitter supplied) Hypoxia in coastal waters is an increasing concern, with the frequency of hypoxic events rising because of climate change and human-driven impacts such as eutrophication. The Atlantic killifish (Fundulus heteroclitus), an estuarine species known for its resilience to environmental stressors, provides a valuable model to investigate the physiological, transcriptional, and epigenetic mechanisms underlying adaptation. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL25254 GPL27461

53 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Purpose: To analyze the toxicity effect of sheepshead minnow larvae exposed to PET microfibers through RNA seq. The expression of specific and sensitive genes on PET microfibers was confirmed and verified through qRT-PCR. Method: RNA was isolated from a sample exposed to PET microfibers (concentration of 10, 100 mg/L) for 10 days using a 72 hpf sheepshead minnow larvae. mRNA was produced with a TruSeq Standed mRNA library kit, and sequencing using a NovaSeq6000 equipment. more...

Organism:

Cyprinodon variegatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29741

4 Samples

Download data: FA, TXT

(Submitter supplied) Live fish transport often results in mass mortality, but the underlying mechanisms are not well known. Largemouth bass (LMB, Micropterus salmoides) juveniles were subjected to 4-hour transportation followed by 5 days of recovery. Mortality (33.61 ± 10.58 %) of the transported fish mainly occurred between 2 and 3 days of recovery. Except for the dead fish, the survivors demonstrating abnormal symptoms were considered more sensitive to the transport stress than the normal ones. more...

Organism:

Micropterus salmoides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34925

68 Samples

Download data: TXT

(Submitter supplied) Predators exert a powerful selective force, however predatoravoidance can conflict with other important activities such as attracting mates. Decisions over whether to court mates versus avoid predators are vital to fitness, yet the mechanistic underpinnings of how animals manage such tradeoffs are poorly understood. Here, we investigate flexibility of behavior and gene regulation in response to a tradeoff between avoiding predators (survival) and courting potential mates (reproduction) in threespined stickleback (Gasterosteus aculeatus). more...

Organism:

Gasterosteus aculeatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30674

62 Samples

Download data: TXT

(Submitter supplied) Molecular, cellular, and organismal alterations are important descriptors of toxic effects, but our ability to extrapolate and predict ecological risks is limited by the availability of studies that link measurable endpoints to adverse population relevant outcomes such as cohort survival and growth. In this study, we used laboratory gene expression and behavior data from two populations of Atlantic killifish Fundulus heteroclitus (one reference site (SCOKF) and one PCB-contaminated site (NBHKF) to inform individual-based models simulating cohort growth and survival from embryonic exposures to environmentally relevant concentrations of neurotoxicants. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34850

36 Samples

Download data: SF

(Submitter supplied) The African turquoise killifish combines a short lifespan with age-dependent loss of neuroregenerative capacity, making it a well-suited model for studying brain repair mechanisms in the context of aging. To investigate the extent of cellular diversity that shapes neuro- and gliogenesis, we performed single cell sequencing of the adult telencephalon. Our analysis identifies seventeen cell types including neuronal cells, and progenitors of glial and non-glial nature. more...

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32658

2 Samples

Download data: MTX, TSV

(Submitter supplied) The mammalian central nervous system (CNS) is susceptible to age-related pathologies, resulting in progressive, irreversible disease. Neurodegenerative eye conditions, like glaucoma and age-related macular degeneneration (AMD), are on the rise due to increased life expectancy. Despite this, there are currently no long-term therapies to prevent degeneration and vision loss. The short-lived African turquoise kililfsh (Nothobranchius furzeri GRZ-AD) is an ideal genetic model for ageing studies, exhibiting rapid ageing phenotypes within its four to six-mont lifespan. more...

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30851

30 Samples

Download data: CSV, TXT

(Submitter supplied) The mammalian central nervous system (CNS) and its retina are susceptible to age-related patholgoies, resulting in progressive, irreversible diseases like glaucoma and age-related macular degeneration (AMD), which are increasingly prevalent with rising life expectancy. Currently, there are no targeted long-term therapies to prevent vision loss. The short lived African turquoise killifsh (Nothobranchius furzeri, GRZ-AD) is a valuable genetic model for ageing studies, displaying rapid ageing phenotypes within its four to six-month lifespan. more...

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32658

6 Samples

Download data: CSV, MTX

(Submitter supplied) A vast body of studies is available that describes age-dependent gene expression in relationship to aging in a number of different model species. These data were obtained from animals kept in conditions with reduced environmental challenges, abundant food and deprivation of natural sensory stimulation. Here we compared wild- and captive-aging in the short-lived turquoise killifish (Nothobranchius furzeri). more...

Organism:

Nothobranchius furzeri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19871

8 Samples

Download data: XLS

(Submitter supplied) Neural crest (NC) is a vertebrate-specific embryonic progenitor cell population at the basis of important vertebrate features such as the craniofacial skeleton and pigmentation patterns. Despite the wide-ranging variation of NC-derived traits across vertebrates, the contribution of NC to species diversification remains underexplored. Here, leveraging the adaptive diversity of African Great Lakes’ cichlid species, we combined comparative transcriptomics and population genomics to investigate the evolution of the NC genetic programme in the context of their morphological divergence. more...

Organism:

Astatotilapia calliptera; Rhamphochromis sp. 'chilingali'

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30104 GPL34016

50 Samples

Download data: TXT

(Submitter supplied) Sex differences in the brain have been demonstrated in all major vertebrate lineages but are not well understood at a molecular and cellular level. Sex-changing fishes provide a unique opportunity to uncover mechanisms underlying sexual differentiation of the brain and regulation of sexual phenotypes. Sex change requires the complete transformation of the gonads and behaviors, which in turn require transformation of sexually-differentiated control mechanisms in the brain. more...

Organism:

Amphiprion ocellaris

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33904

4 Samples

Download data: RDS

(Submitter supplied) Despite deep evolutionary conservation, recombination varies greatly across the genome, among individuals, sexes and populations and can be a major evolutionary force in the wild. Yet this variation in recombination and its impact on adaptively diverging populations is not well understood. To elucidate the nature and potential consequences of recombination rate variation, we characterized fine-scale recombination landscapes by combining pedigrees, functional genomics and field fitness measurements in an adaptively divergent pair of marine and freshwater threespine stickleback populations from River Tyne, Scotland. more...

Organism:

Gasterosteus aculeatus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34145

12 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) The mangrove killifish, Kryptolebias marmoratus, can reproduce with self-fertilisation, offering a unique and useful genetic tool for generation of genetic mutants and quick identification of mutated genes. From an ENU-mutated mangrove killifish line R228, we have isolated a novel mutant line, no-fin-ray/nfr in which homozygous mutant of adult fish fin ray development is largely reduced. Besides the reduction of the fin, the nfr mutant also exhibited other phenotype associated with ectodermal cell lineages including loss of scales, deformation in the gill structure such as decreasing the number of gill filaments, the reduction in the number of jaw teeth, pharyngeal teeth and gill rakers. more...

Organism:

Kryptolebias marmoratus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23686

12 Samples

Download data: FA, TSV

(Submitter supplied) Sex differentiation is a complex process that requires many factors to regulate proliferation, differentiation, development, and organization of the gonads. In teleosts, the molecular mechanisms of sex differentiation are diverse and unclear, especially in hermaphrodite fish. In the present study, 15 cell types, including germ cells, follicle cells, and theca cells, and so on, were identified using single-cell RNA sequencing (scRNA-seq) in the gonads during sex differentiation in a hermaphrodite fish, orange-spotted grouper (Epinephelus coioides). more...

Organism:

Epinephelus coioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32885

6 Samples

Download data: FA, MTX, TSV

(Submitter supplied) Determining the physiological effects of parasites and characterizing genes involved in host responses to infections are essential to improving our understanding of host-parasite interactions and their ecological and evolutionary consequences. This task, however, is complicated by high diversity and complex life histories of many parasite species. The use of transcriptomics in the context of wild-caught specimens can help ameliorate this by providing both qualitative and quantitative information on gene expression patterns in response to parasites in specific host organs and tissues. more...

Organism:

Perca fluviatilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33588

22 Samples

Download data: TXT