GEO DataSets

(Submitter supplied) Background: Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of human biomedical science. Many such classifiers discovered thus far lack vigorous statistical and experimental validations, with their stability and reliability unknown. A combination of genetic algorithm/support vector machines and genetic algorithm/K nearest neighbors were used in this study to search for classifiers of endocrine disrupting chemicals (EDCs) in zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platforms:

GPL7301 GPL7244 GPL7302

318 Samples

Download data: TXT

(Submitter supplied) Background: Complex biological networks control fundamental processes such as reproduction. The relationship of network structure to biological function was investigated in a global gene interaction network developed from ovary tissues of the model fish, fathead minnow (Pimephales promelas). Results: A global ovary gene interaction network was inferred from gene expression in ovaries of fathead minnow representing 288 different exposure conditions and 1,472 microarrays. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

1470 Samples

Download data: TXT

(Submitter supplied) Modeled on human connectivity mapping (Cmap), this study was undertaken to investigate the potential applications of Cmap approach in ecotoxicology. Over 3500 zebrafish (Danio rerio) and fathead minnow (Pimephales promelas) transcriptomic profiles, each associated with one of several dozen chemical treatment conditions, were compiled into three distinct collections of rank-ordered gene lists (ROGLs) by species and microarray platforms. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platforms:

GPL9248 GPL15775

580 Samples

Download data: TXT

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

Organism:

Pimephales promelas

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL10259

511 Samples

Download data: TXT

(Submitter supplied) Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. more...

Organism:

Danio rerio

Type:

Third-party reanalysis; Expression profiling by array

Download data: TXT

(Submitter supplied) Fathead minnow and zebrafish are among the most intensively studied fish species in environmental toxicogenomics. To aid the assessment and interpretation of subtle transcriptomic effects from treatment conditions of interest, there needs to be a better characterization and understanding of the natural variation in gene expression among fish individuals within populations. Little effort, however, has been made in this area. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

511 Samples

Download data: TXT

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

Organism:

Pimephales promelas; Danio rerio

Type:

Expression profiling by array

Platforms:

GPL6457 GPL9248

66 Samples

Download data: TXT

(Submitter supplied) Effects of bisphenol A (BPA) on ovarian transcript profiles as well as targeted endpoints with endocrine/reproductive relevance were examined in two fish species, fathead minnow (Pimephales promelas) and zebrafish (Danio rerio), exposed in parallel using matched experimental designs. Four days of waterborne exposure to 10 µg BPA caused significant vitellogenin induction in both species. However, zebrafish were less sensitive to effects on hepatic gene expression and steroid production than fathead minnow and the magnitude of vitellogenin induction was more modest. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL9248

32 Samples

Download data: TXT

(Submitter supplied) Effects of bisphenol A (BPA) on ovarian transcript profiles as well as targeted endpoints with endocrine/reproductive relevance were examined in two fish species, fathead minnow (Pimephales promelas) and zebrafish (Danio rerio), exposed in parallel using matched experimental designs. Four days of waterborne exposure to 10 µg BPA caused significant vitellogenin induction in both species. However, zebrafish were less sensitive to effects on hepatic gene expression and steroid production than fathead minnow and the magnitude of vitellogenin induction was more modest. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

34 Samples

Download data: TXT

(Submitter supplied) Paper Abstract. Extrapolating toxicological sensitivity information across species can require the use of highly conservative safety factors as prescribed by ecological risk assessment protocols. The objective of our study was to use multipule factors to understand the dynamics of stress responses by comparing ecotoxicological, developmental, and genomic data to quantitatively determine the relative sensitivity of two common model aquatic vertebrates to assess the potential for developing refined safety factors among species. more...

Organism:

Danio rerio; Pimephales promelas

Type:

Expression profiling by array

Platforms:

GPL7301 GPL10259

59 Samples

Download data: TXT

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

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

23 Samples

Download data: TXT

(Submitter supplied) Diethylstilbestrol (DES) is a synthetic estrogen that has been banned for use in humans, but still is employed in livestock and aquaculture operations in some parts of the world. Detectable concentrations of DES in effluent and surface waters have been reported to range from slightly below 1 to greater than 10 ng/L. Little is known, however, concerning the toxicological potency of DES in fish. In this study, sexually-mature fathead minnows (Pimephales promelas) of both sexes were exposed to 1, 10 or 100 ng DES/L water in a flow-through system. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

11 Samples

Download data: TXT

(Submitter supplied) Diethylstilbestrol (DES) is a synthetic estrogen that has been banned for use in humans, but still is employed in livestock and aquaculture operations in some parts of the world. Detectable concentrations of DES in effluent and surface waters have been reported to range from slightly below 1 to greater than 10 ng/L. Little is known, however, concerning the toxicological potency of DES in fish. In this study, sexually-mature fathead minnows (Pimephales promelas) of both sexes were exposed to 1, 10 or 100 ng DES/L water in a flow-through system. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

12 Samples

Download data: TXT

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

Organism:

Danio rerio; Pimephales promelas

Type:

Expression profiling by array

Platforms:

GPL7282 GPL6563

24 Samples

Download data: TXT

(Submitter supplied) This experiment was conducted as part of an overall study aimed at examining effects of a dopamine receptor antagonist on reproduction, behavior, and gene expression in cyprinid fish. Relative to gene expression, we hypothesized that if haloperidol disrupted normal regulation of the HPG axis, there may be robust transcriptional alterations in the ovary of exposed females that might serve as useful markers of exposure and/or effects. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL7282

12 Samples

Download data: TXT

(Submitter supplied) This experiment was conducted as part of an overall study aimed at examining effects of a dopamine receptor antagonist on reproduction, behavior, and gene expression in cyprinid fish. Relative to gene expression, we hypothesized that if haloperidol disrupted normal regulation of the HPG axis, there may be robust transcriptional alterations in the ovary of exposed females that might serve as useful markers of exposure and/or effects. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6563

12 Samples

Download data: TXT

(Submitter supplied) Omics approaches are broadly used to explore endocrine and toxicity-related pathways and functions. Nevertheless, there is still a significant gap in knowledge in terms of understanding the endocrine system and its numerous connections and intricate feedback loops, especially in non-model organisms. The main purpose of this analysis was to generate tissue-specific omics data in order to support future aquatic ecotoxicogenomic and endocrine-related studies as well as to improve our understanding of the fathead minnow as an ecological model.

Organism:

Pimephales promelas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25572

12 Samples

Download data: FASTA, TXT

(Submitter supplied) We evaluated the possible mechanisms by which exposure to a sequentially treated pulp and paper mill effluent affects gene expression in the liver of male and female fathead minnows.

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL7282

24 Samples

Download data: TXT

(Submitter supplied) According to the developmental origins of health and disease (DOHaD) hypothesis, exposure to environmental stressors during early development can cause genetic, epigenetic, or functional changes in tissues that increase disease risk later in life. Atrazine (ATZ) is a commonly used pesticide that frequently contaminates rural and urban water sources at levels above the 3 ppb maximum contaminant level set by the US Environmental Protection Agency. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL23074

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Prochloraz is a fungicide known to cause endocrine disruption through effects on the hypothalamic-pituitary-gonadal (HPG) axis. To determine the short-term impacts of prochloraz on gene expression and steroid production, adult female fathead minnows (Pimephales promelas) were exposed to the chemical (0 or 300 μg/L) for a time-course of 6, 12 and 24 h. Consistent with inhibition of cytochrome P450 17α-hydroxylase/17,20-lyase (CYP17) and aromatase (CYP19), known molecular targets of prochloraz, plasma 17β-estradiol (E2) was reduced within 6 hours. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL9248

23 Samples

Download data: TXT