title: Microarray analysis of zebrafish cloche mutant using amplified cDNA and identification of potential downstream target genes.
abstract: Zebrafish is an excellent model organism for studying vertebrate development and human disease. With the availability of increased numbers of zebrafish mutants and microarray chips, gene expression profiling has become a powerful tool for identification of downstream target genes perturbed by a specific mutation. One of the obstacles often encountered, however, is to isolate large numbers of zebrafish mutant embryos that are indistinguishable in morphology from the wild-type siblings for microarray analysis. Here, we report a method using amplified cDNA derived from five embryos for gene expression profiling of the 18-somite zebrafish cloche (clo) mutant, in which development of hematopoietic and endothelial lineages is severely impaired. In total, 31 differentially expressed target genes are identified, of which 13 have not been reported previously. We further determine that of these 13 new targets, 8 genes, including coproporphyrinogen oxidase (cpo), carbonic anhydrase (cahz), claudin g (cldn g), zinc-finger-like gene 2 (znfl2), neutrophil cytosol factor 1 (ncf1), matrix metalloproteinase 13 (mmp13), dual specificity phosphatase 5 (dusp5), and a novel gene referred as zebrafish vessel-specific gene 1 (zvsg1) are predominantly expressed in hematopoietic and endothelial cells. Comparative analysis demonstrates that this method is comparable and complementary to that of the conventional approach using unamplified sample. Our study provides valuable information for studying hematopoiesis and vessel formation. The method described here offers a powerful tool for gene expression profiling of zebrafish mutants in general.
authors.affiliation: Laboratory of Molecular and Developmental Immunology, Institute of Molecular and Cell Biology, Proteos, Singapore.
authors.forename: Feng
authors.initials: F
authors.lastname: Qian
authors.forename: Fenghua
authors.initials: F
authors.lastname: Zhen
authors.forename: Chinthing
authors.initials: C
authors.lastname: Ong
authors.forename: Suk-Won
authors.initials: SW
authors.lastname: Jin
authors.forename: Hui
authors.initials: H
authors.lastname: Meng Soo
authors.forename: Didier Y R
authors.initials: DY
authors.lastname: Stainier
authors.forename: Shuo
authors.initials: S
authors.lastname: Lin
authors.forename: Jinrong
authors.initials: J
authors.lastname: Peng
authors.forename: Zilong
authors.initials: Z
authors.lastname: Wen
mesh_terms: D000818:Animals; D018076:DNA, Complementary / Q000235:genetics*; D015536:Down-Regulation; D004625:Embryo, Nonmammalian / Q000196:embryology / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D005838:Genotype; D006720:Homozygote; D009154:Mutation / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D019170:Somites / Q000378:metabolism; D015027:Zebrafish / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D029961:Zebrafish Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D029961:Zebrafish Proteins