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.
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
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes