GEO DataSets

(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; Phalacrocorax auritus; Pimephales promelas; Lithobates pipiens

Type:

Expression profiling by high throughput sequencing

9 related Platforms

724 Samples

Download data: TXT

(Submitter supplied) Modern 21st century toxicity testing makes use of omics technologies to address critical questions in toxicology and chemical management. Of interest are questions relating to chemical mechanisms of toxicity, differences in species sensitivity, and translation of molecular effects to observable apical endpoints. Our study addressed these questions by comparing apical outcomes and multiple omics responses in early-life stage exposure studies with Japanese quail (JQ; Coturnix japonica) and double crested cormorant (DCCO; Phalacrocorax auritus), representing a model and ecological species, respectively. more...

Organism:

Phalacrocorax auritus; Coturnix japonica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30378 GPL29437

29 Samples

Download data: TXT

(Submitter supplied) Species difference in susceptibility to toxicants is a critical issue in ecotoxicology. Transcriptomics is being proposed as a strategy to improve toxicity testing for regulatory risk assessment; however, different responses among species have not been extensively explored using this approach. In the present study, we identified dysregulated genes and pathways in Japanese quail (JQ) and double-crested cormorant (DCCO) embryos following exposure to ethinylestradiol (EE2). more...

Organism:

Phalacrocorax auritus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32719

15 Samples

Download data: TXT

(Submitter supplied) Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). more...

Organism:

Coturnix japonica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29437

15 Samples

Download data: TXT

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

Organism:

Coturnix japonica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29437 GPL29461

31 Samples

Download data

(Submitter supplied) Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). more...

Organism:

Coturnix japonica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29461

16 Samples

Download data: TXT

(Submitter supplied) Investigation of mRNA expression (using HiSeq 2500) in response to treatment of Daphnia magna to pyriproxyfen, wetland water, or stormwater samples.

Organism:

Daphnia magna

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23821

230 Samples

Download data: TXT

(Submitter supplied) Triclocarban (TCC) is a widely used antimicrobial agent that is routinely detected in surface waters. The present study was designed to examine TCC’s efficacy and mode of action as a reproductive toxicant in fish. Reproductively mature Pimephales promelas were continuously exposed to either 1 or 5 μg TCC/L, 0.5 μg 17β-trenbolone (TRB)/L or a mixture (MIX) of 5 μg TCC and 0.5 μg TRB/L for 22 d and a variety of reproductive and endocrine-related endpoints were examined. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL10259

24 Samples

Download data: TXT

(Submitter supplied) The increasing application of RNA-seq to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based tool for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. ExpressAnalyst contains a series of modules that enable raw data processing and annotation of FASTQ files, and statistical and functional analysis of counts tables and gene lists. more...

Organism:

Homarus americanus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33161

19 Samples

Download data: TXT

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

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platforms:

GPL17098 GPL15775

80 Samples

Download data: TXT

(Submitter supplied) Microarrays are used to assess the impacts of aquatic contaminants in both laboratory and field studies, which necessitates the validation of the comparability of microarray data generated by different laboratories before this tool is adopted for regulatory toxicology or environmental monitoring. Fundamental issues which need answering before microarray technology can be used in environmental monitoring programs include defining whether these molecular changes translate into adverse effect at the individual or population level, as well as how large a magnitude (threshold) and how to quantify (fold change versus p value) a modification or modifications in gene expression which constitute an adverse effect. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

16 Samples

Download data: TXT

(Submitter supplied) Microarrays are used to assess the impacts of aquatic contaminants in both laboratory and field studies, which necessitates the validation of the comparability of microarray data generated by different laboratories before this tool is adopted for regulatory toxicology or environmental monitoring. Fundamental issues which need answering before microarray technology can be used in environmental monitoring programs include defining whether these molecular changes translate into adverse effect at the individual or population level, as well as how large a magnitude (threshold) and how to quantify (fold change versus p value) a modification or modifications in gene expression which constitute an adverse effect. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL17098

16 Samples

Download data: TXT

(Submitter supplied) Microarrays are used to assess the impacts of aquatic contaminants in both laboratory and field studies, which necessitates the validation of the comparability of microarray data generated by different laboratories before this tool is adopted for regulatory toxicology or environmental monitoring. Fundamental issues which need answering before microarray technology can be used in environmental monitoring programs include defining whether these molecular changes translate into adverse effect at the individual or population level, as well as how large a magnitude (threshold) and how to quantify (fold change versus p value) a modification or modifications in gene expression which constitute an adverse effect. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

16 Samples

Download data: TXT

(Submitter supplied) Microarrays are used to assess the impacts of aquatic contaminants in both laboratory and field studies, which necessitates the validation of the comparability of microarray data generated by different laboratories before this tool is adopted for regulatory toxicology or environmental monitoring. Fundamental issues which need answering before microarray technology can be used in environmental monitoring programs include defining whether these molecular changes translate into adverse effect at the individual or population level, as well as how large a magnitude (threshold) and how to quantify (fold change versus p value) a modification or modifications in gene expression which constitute an adverse effect. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

16 Samples

Download data: TXT

(Submitter supplied) Microarrays are used to assess the impacts of aquatic contaminants in both laboratory and field studies, which necessitates the validation of the comparability of microarray data generated by different laboratories before this tool is adopted for regulatory toxicology or environmental monitoring. Fundamental issues which need answering before microarray technology can be used in environmental monitoring programs include defining whether these molecular changes translate into adverse effect at the individual or population level, as well as how large a magnitude (threshold) and how to quantify (fold change versus p value) a modification or modifications in gene expression which constitute an adverse effect. more...

Organism:

Pimephales promelas

Type:

Expression profiling by array

Platform:

GPL15775

16 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) Objective: To study post-hatching development after transfer of morphologically good quality embryos that survived in vitro maturation under lipolytic conditions using a well-established and recognized bovine model. Design: prospective study with a crossover design. Setting: research laboratory. Animals: 8 healthy multiparous non-lactating Holstein cows used in repeated embryo transfers. Intervention(s): Bovine cumulus oocyte complexes (COCs) were in vitro matured in the presence of either 1) a combination of elevated pathophysiological concentration of palmitic acid (PA) and physiological concentrations of stearic acid (SA) and oleic acid (OA) (HIGH PA), or 2) physiological concentrations of PA, SA and OA (BASAL). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22316

53 Samples

Download data: TXT

(Submitter supplied) Comparison of gene expression of exposed versus non-exposed Oncorhynchus mykiss hepatocytes to four model chemicals and a synthetic mixture. Hepatocytes were exposed for 24 hours to a single chemical and a synthetic mixture of 10 nM 17 alpha-ethinylestradiol (EE2), 0.75 nM 2,3,7,8-tetrachloro-di-benzodioxin (TCDD), 100 μM paraquat and 0.75 μM 4-nitroquinoline-1-oxide (NQO). Keywords: Exposed vs. control

Organism:

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

Type:

Expression profiling by array

Platform:

GPL2716

40 Samples

Download data: TXT

(Submitter supplied) RNA-seq expression assays were done in larval Pimephales promelas (Fathead minnow, FHM) exposed to 10 chemicals (3 metals, 4 Neonicotinoids, and 3 pharmaceuticals) over a range of concentrations to derive relatively short term transcriptomics based points of departure (tPODs). tPODs were compared to apical points of departures (aPODs) to investigate the potential use of the FHM tPODS as part of a high throughput approach that might be used in a regulatory context.

Organism:

Pimephales promelas

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25572

878 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