PUBLICATION
Global gene expression analysis using a zebrafish oligonucleotide microarray platform
- Authors
- Peterson, S.M., and Freeman, J.L.
- ID
- ZDB-PUB-090819-10
- Date
- 2009
- Source
- Journal of visualized experiments : JoVE (30): (Journal)
- Registered Authors
- Freeman, Jennifer, Peterson, Sam
- Keywords
- none
- MeSH Terms
-
- Animals
- Carbocyanines/chemistry
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Fluorescent Dyes/chemistry
- Gene Expression Profiling/methods*
- Nucleic Acid Hybridization
- Oligonucleotide Array Sequence Analysis/methods*
- Zebrafish/genetics*
- Zebrafish/metabolism
- PubMed
- 19684566 Full text @ J. Vis. Exp.
Citation
Peterson, S.M., and Freeman, J.L. (2009) Global gene expression analysis using a zebrafish oligonucleotide microarray platform. Journal of visualized experiments : JoVE. (30).
Abstract
Gene microarray technology permits quantitative measurement and gene expression profiling of transcript levels on a genome-wide basis. Gene microarray technology is used in numerous biological disciplines in a variety of applications including global gene expression analysis in relation to developmental stage, to a disease state, and in toxic responses. Herein, we include a demonstration of global gene expression analysis using a comprehensive zebrafish-specific oligonucleotide microarray platform. The zebrafish expression microarray platform contains 385,000 probes, 60 base pairs in length, interrogating 37,157 targets with up to 12 probes per target. For this platform, all cDNA and genomic information available for the zebrafish was collected from various genomic databases including Ensembl (http://www.ensembl.org), VEGA (http://vega.sanger.ac.uk), UCSC (http://genome.ucsc.edu), and ZFIN (http://www.zfin.org). As a result this expression array provides complete coverage of the current zebrafish transcriptome. The zebrafish expression microarray was printed by Roche NimbleGen (Madison, WI). This technical demonstration includes the fluorescent labeling of a cDNA product, hybridization of the labeled cDNA product to the microarray platform, and array scanning for signal acquisition using the one color analysis strategy.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping