PUBLICATION

DNA microarray application in ecotoxicology: experimental design, microarray scanning, and factors impacting transcriptional profiles in a small fish species

Authors
Wang, R.L., Biales, A., Bencic, D., Lattier, D., Kostich, M., Villeneuve, D., Ankley, G.T., Lazorchak, J., and Toth, G.
ID
ZDB-PUB-071118-38
Date
2008
Source
Environmental toxicology and chemistry   27(3): 652-663 (Journal)
Registered Authors
Biales, Adam
Keywords
none
MeSH Terms
  • Animals
  • Brain/drug effects
  • Brain/metabolism
  • Environmental Monitoring/methods*
  • Ethinyl Estradiol/toxicity
  • Fadrozole/toxicity
  • Female
  • Gene Expression Profiling/methods*
  • Male
  • Oligonucleotide Array Sequence Analysis*
  • Ovary/drug effects
  • Ovary/metabolism
  • Testis/drug effects
  • Testis/metabolism
  • Transcription, Genetic*
  • Trenbolone Acetate/toxicity
  • Water Pollutants, Chemical/toxicity*
  • Zebrafish/genetics
  • Zebrafish/metabolism*
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism
PubMed
17990945 Full text @ Environ. Toxicol. Chem.
Abstract
The research presented here is part of a larger study of the molecular mode of action of endocrine disrupting chemicals targeting the hypothalamic-pituitary-gonadal axis in zebrafish (Danio rerio). It addresses several issues critical to microarray application in aquatic ecotoxicology: experimental design, microarray scanning, gene expression intensity distribution, and the impact of experimental parameters on the zebrafish transcriptome. Expression profiles from various tissues of individual zebrafish exposed to 17alpha-ethinyl estradiol, fadrozole, or 17beta-trenbolone for 48 or 96 h were examined using the Agilent Oligo Microarray (G2518A). As a flexible and efficient alternative to the designs commonly used in microarray studies, an "unbalanced incomplete block" design was found well-suited for this work as evidenced by high data reproducibility, low microarray to microarray variability, and little gene-specific dye bias. Random scanner noise had little effect on data reproducibility. A low level, slightly variable Cy3 contaminant was revealed by hyperspectral imaging, suggesting fluorescence contamination as a potential contributor to the large variance associated with weakly expressed genes. Expression intensities of zebrafish genes were skewed toward the lower end of their distribution range, and more weakly expressed genes tended to have larger variances. Tissue type, followed in descending order by gender, chemical treatment, and exposure duration, had the greatest impact on the overall gene expression profiles, a finding potentially critical to experimental design optimization. Overall, there was excellent congruence between quantitative polymerase chain reaction results and microarray profiles of 13 genes examined across a subset of 20 pairs of ovarian samples. These findings will help to improve applications of microarrays in future ecotoxicological studies.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping