GEO DataSets

(Submitter supplied) The human transcription factor (TF) CGGBP1 (“CGG Binding Protein”) is conserved only in amniotes, and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we examine the DNA binding preferences of a wide variety of metazoan CGGBP1-like TFs with this bipartite domain using PBM experiments. The derived motifs are available at ...

Organism:

Petromyzon marinus; Acipenser ruthenus; Gallus gallus; Erpetoichthys calabaricus; Rhizophagus irregularis; Paramormyrops kingsleyae; Acyrthosiphon pisum; Salmo salar; Fundulus heteroclitus; Sparus aurata; Chrysemys picta; Austrofundulus limnaeus; Anabas testudineus; Amphiprion percula; Salarias fasciatus; Locusta migratoria; Crocodylus porosus; Homo sapiens; Rhodnius prolixus; Rhipicephalus appendiculatus; Kryptolebias marmoratus; Nematostella vectensis; Acanthochromis polyacanthus; Hippocampus comes; Hofstenia miamia; Aedes aegypti; Culex quinquefasciatus; Latimeria chalumnae; Cyprinus carpio; synthetic construct; Hucho hucho; Amphiprion ocellaris; Labeo rohita; Mola mola; Sphaeramia orbicularis; Anabarilius grahami

Type:

Other

Platform:

GPL11260

258 Samples

Download data: TXT

(Submitter supplied) Embryos from 8 populations of killifish, four with evolved tolerances, were exposed to PCB-126. Approximately 5 replicate embryos per treatment/control were sequenced. Desensitization of aryl hydrocarbon receptor signaling to PCB-126 is found in all four populations with evolved pollution tolerance, and represents the strongest transcriptional difference between tolerant and sensitive populations.

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29035

75 Samples

Download data: TXT

(Submitter supplied) Adult fish produce new cells throughout their central nervous system during the course of their lives. Furthermore, they maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received comparatively little attention. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27461

20 Samples

Download data: TXT

(Submitter supplied) The goal was to determine differences in gene expression of 384 metabolic genes during late organogenesis among embryos of parents from a clean site (Magotha Bay, VA) and polluted site (Elizabeth RIver, VA). Hybrid gene expression was examined to explore parental effect. Embryo morphology and heart rate during late organogenesis and pre-hatching was assessed in order to determine phenotypic differences between embryo groups.

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL26931

40 Samples

Download data: TXT

(Submitter supplied) Although alternative Flame Retardant (FR) chemicals are expected to be safer than the legacy FRs they replace, their risks to human health and the environment are often poorly characterized. This study used a small volume, fish embryo system to reveal potential mechanisms of action and diagnostic exposure patterns for TBPH (bis (2-ethylhexyl)-tetrabromophthalate), a component of several widely-used commercial products. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25254

48 Samples

Download data: TXT

(Submitter supplied) To explore how gene expression translates to developmental phenotype in both sensitive and resistant Fundulus embryos upon POP exposure, we exposed Fundulus embryos from the Elizabeth River Superfund population and the Magotha Bay, VA clean population to Elizabeth River polluted sediment extracts and measured chemical uptake, gene expression, and altered embryo anatomy, morphology and cardiac physiology during four critical developmental stages: somitogenesis, heart beat initiation, late organogenesis, and pre-hatching.

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL10430

64 Samples

Download data: TXT

(Submitter supplied) The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model due to its ability to acclimate to rapid environmental changes and adapt to polluted habitats. Killifish respond to rapid increases in salinity with an immediate change in gene expression, as well as long-term remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit the ability of killifish gill to respond to a rapid increase in salinity. more...

Organism:

Fundulus heteroclitus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25194

24 Samples

Download data: FA, TXT

(Submitter supplied) Killifish (Fundulus heteroclitus) inhabiting the New Bedford Harbor (NBH) Superfund Site have evolved resistance to the toxic and biochemical effects of non-ortho (dioxin-like) polychlorinated biphenyls (DL-PCBs) and other compounds that act via the aryl hydrocarbon receptor (AHR) signaling pathway. However, the majority of PCBs in NBH are ortho-substituted (non-DL) PCBs (o-PCBs), and the impacts of these o-PCBs on fish populations are not well understood. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25194

20 Samples

Download data: TXT

(Submitter supplied) Gene expression was measured in the gills of saltwater (SW) acclimated Atlantic Killifish, Fundulus heteroclitus, over a time course of freshwater (FW) exposure, in which half the fish were exposed to arsenic. Fish were sampled from three populations, two from Maine, USA (ME) and one from Virginia, USA (VA)

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL14994

72 Samples

Download data: PAIR, TXT

(Submitter supplied) RNA from PCB-126 exposed 10 days post-fertilization (dpf) embryos were sequenced to characterize the chemical exposure response of killifish from a PCB-resistant population (NBH, New Bedford Harbor, MA, Superfund site) as compared to a reference (SC, Scorton Creek, MA) population. Since the genome sequence was not available, we also performed shot-gun sequencing of RNA from 1-15 dpf embryos sampled every day from both populations to serve as a transcriptome assembly. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22406

6 Samples

Download data: FNA, XLSX

(Submitter supplied) The Atlantic killifish (Fundulus heteroclitus) is an ideal model species to study physiological and toxicological adaptations to stressors. Killifish inhabiting the PCB-contaminated Superfund site in New Bedford Harbor, MA (NBH) have evolved resistance to toxicity and activation of the aryl hydrocarbon receptor (AHR) signaling pathway after exposure to PCBs and other AHR agonists. Until recently, a lack of genomic information has limited efforts to understand the molecular mechanisms underlying environmental adaptation to stressors. more...

Organism:

Fundulus heteroclitus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20697

4 Samples

Download data: BED, FASTA, TXT

(Submitter supplied) Global climate change increasingly polarizes environments, presenting unprecedented challenges to many organisms (Smol, 2012). Polarization occurs not only in the spatial dimension, producing greater desert drought and tropical rainfall, for example, but also in the temporal dimension by making a local environment more variable over time. Many organisms survive these fluctuating environmental conditions by manifesting multiple distinct phenotypes through developmental processes that enable phenotypic plasticity (Pigliucci et al., 2006; Parsons et al., 2011). more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL14994

36 Samples

Download data: PAIR

(Submitter supplied) This study explores the synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (β-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (α-naphthoflavone), on gene expression in stage 31 embryos from two different population. One population (Elizabeth River population) is relatively resistant to the pollutants in its environment.

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL10430

48 Samples

Download data: TXT

(Submitter supplied) To better assess the impact of contaminants on fish reproduction, it is increasingly important to collect data at multiple levels of biological organization. However, a challenge in ecotoxicology is that three of the most commonly measured reproductive endpoints; gonad histology, ex vivo steroid production, and gene expression, can be difficult to obtain in small-bodied fish (e.g. zebrafish, Japanese medaka, fathead minnow) due to limited tissue availability. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL17413

8 Samples

Download data: TXT

(Submitter supplied) Temperature profoundly affects biological systems across all levels of organization. Over generations, species become evolutionarily adapted to specific thermal environments. In addition to evolved adaptive differences, individuals may reversibly modify their phenotype within their lifetimes in response to different thermal environments in a process termed phenotypic plasticity. The interaction between, evolutionary adaptation and phenotypic plasticity is complex and contentious. more...

Organism:

Fundulus heteroclitus; Fundulus grandis

Type:

Expression profiling by array

Platform:

GPL10430

113 Samples

Download data: TXT

(Submitter supplied) The objective of this study was to gain mechanistic insight into how mummichog are able to produce eggs during exposures to high levels of EE2. Mummichog were exposed to 0, 50 or 250 ng/L of EE2 for 14 d. A mummichog microarray was used to identify genomic responses associated with high EE2 exposure, and effects of EE2 on target genes involved in lipid mobilization and transport and steroidogenesis, two important (EE2 regulated) pathways involved in egg production, were measured using real-time PCR. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL17413

15 Samples

Download data: TXT

(Submitter supplied) The changes in the transcriptome of Fundulus heteroclitus embryos incubated in water or in air from the blastula stage was investigated.

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL9786

42 Samples

Download data: TXT

(Submitter supplied) The present study used microarray expression profiling to determine the effects of embryonic arsenic exposure. Fertilized killifish (Fundulus heteroclitus) eggs were exposed to 0, 5, 15, or 25ppm arsenic as sodium arsenite. To examine differentially expressed genes, the microarrays were probed using RNA obtained from the control and 25ppm-exposed killifish just after hatching. No differences were noted in survival or hatching success between any of the groups. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL13723

20 Samples

Download data: TXT

(Submitter supplied) This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL10430

72 Samples

Download data: TXT

(Submitter supplied) This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage. Patterns of gene expression for 7,000 genes appear to be important as they recapitulate developmental timing. Among the 45% of genes with significant expression differences between pairs of temporally adjacent stages, significant differences in gene expression vary from as few as five to more than 660. more...

Organism:

Fundulus heteroclitus

Type:

Expression profiling by array

Platform:

GPL10430

160 Samples

Download data: TXT