Microarray gene expression profiling during the segmentation phase of zebrafish development

Linney, E., Dobbs-McAuliffe, B., Sajadi, H., and Malek, R.L.
Comparative biochemistry and physiology. Toxicology & pharmacology : CBP   138(3): 351-362 (Journal)
Registered Authors
Dobbs-McAuliffe, Betsy, Linney, Elwood
Development; Gene expression; Microarray; Myogenesis; Somite; Embryo; RT-PCR; Zebrafish; Oligonucleotide
MeSH Terms
  • Animals
  • Cluster Analysis
  • Cytochrome P-450 Enzyme System/metabolism
  • Embryo, Nonmammalian/embryology
  • Embryo, Nonmammalian/metabolism
  • Gene Expression Profiling*/standards
  • Gene Expression Regulation, Developmental*
  • In Situ Hybridization
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis*/standards
  • Quality Control
  • RNA, Messenger/analysis
  • Reproducibility of Results
  • Time Factors
  • Zebrafish/embryology*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics*
15533793 Full text @ Comp. Biochem. Physiol. C Toxicol. Pharmacol.
We analyzed 15,512 unique transcripts from wild-type Danio rerio using a long oligonucleotide microarray containing >16,000 65-mers probes. Total RNA was isolated from staged embryos at 2 h intervals over a 24-h period. On average, at any given time point, 27% of the probe set detected corresponding transcripts in embryonic RNA. There were two predominant patterns in the nearly 4000 genes that changed expression in at least one time point during the first 24 hpf. At 12 hpf, we detected 420 up-regulated and 386 down-regulated genes. By 24 hpf, the number of up- and down-regulated genes had increased to 954 and 766, respectively. While the majority of these genes maintained their new level of expression for the duration of the time course, we identified five genes with phasic regulation over the 24-h time course. Two of these genes, germ cell nuclear factor and mesogenin, have been identified as being expressed during gastrulation (5 1/4 to 10 h postfertilization) and subsequently repressed. A cluster containing 36 distinct ribosomal proteins was up-regulated at 12 h, indicating a capability for de novo protein synthesis during and after this stage. Twenty-three muscle-specific genes were up-regulated late during the initial 24 hpf, corresponding to the development and differentiation of the somites.
Genes / Markers
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Engineered Foreign Genes
Errata and Notes