ZFIN ID: ZDB-PUB-080728-1
High-throughput whole mount in situ hybridization of zebrafish embryos for analysis of tissue-specific gene expression changes after environmental perturbation
Coverdale, L.E., Burton, L.E., and Martin, C.C.
Date: 2008
Source: Methods in molecular biology (Clifton, N.J.)   410: 3-14 (Chapter)
Registered Authors: Burton, Lindsay, Martin, C. Cristofre
Keywords: none
MeSH Terms:
  • Animals
  • Cadmium/toxicity
  • Embryo, Nonmammalian/embryology
  • Embryo, Nonmammalian/metabolism*
  • Environmental Pollutants/toxicity
  • Gene Expression Profiling/instrumentation
  • Gene Expression Profiling/methods*
  • Gene Expression Regulation, Developmental/drug effects
  • In Situ Hybridization/instrumentation
  • In Situ Hybridization/methods*
  • Zebrafish/embryology
  • Zebrafish/genetics*
PubMed: 18642591 Full text @ Meth. Mol. Biol.
Whole mount in situ hybridization is a process that allows the visualization of gene expression (mRNA) within the cells of an intact organism. By comparing gene expression domains between organisms that have been subjected to different environmental conditions, an understanding of the cellular and tissue-specific effects of these environmental exposures can be identified. This technique is complementary to gene expression profiling techniques such as DNA microarrays which can usually provide information only on the differential levels of gene expression within an organism or tissue. In the case of whole mount in situ hybridization there is the added ability to detect differences in the distribution of cells, within a whole organism, expressing a particular gene. Subtle changes in the distribution of cells expressing a gene may not be reflected in the overall level of gene expression when RNA samples are retrieved from a whole organism and assayed. Exploitation of automation technology has made whole mount in situ hybridization a procedure that is amiable to high-throughput genomic studies. Combining automation with computer-aided image analysis makes this an efficient strategy for quantifying subtle changes in tissues and genes expression that can result from sublethal exposures to environmental toxins, for example.