Application of chicken microarrays for gene expression analysis in other avian species

Abstract

BackgroundWith the threat of emerging infectious diseases such as avian influenza, whose natural hosts are thought to be a variety of wild water birds including duck, we are armed with very few genomic resources to investigate large scale immunological gene expression studies in avian species. Multiple options exist for conducting large gene expression studies in chickens and in this study we explore the feasibility of using one of these tools to investigate gene expression in other avian species.ResultsIn this study we utilised a whole genome long oligonucleotide chicken microarray to assess the utility of cross species hybridisation (CSH). We successfully hybridised a number of different avian species to this array, obtaining reliable signals. We were able to distinguish ducks that were infected with avian influenza from uninfected ducks using this microarray platform. In addition, we were able to detect known chicken immunological genes in all of the hybridised avian species.ConclusionCross species hybridisation using long oligonucleotide microarrays is a powerful tool to study the immune response in avian species with little available genomic information. The present study validated the use of the whole genome long oligonucleotide chicken microarray to investigate gene expression in a range of avian species.

Peer Review #2 of "Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasite Neospora caninum (v0.1)"

“…gregaria) species using a whole genome oligonucleotide microarray of the fruit fly Drosophila melanogaster. In line with previous studies in mammalian (Nieto-Díaz et al, 2007) and avian hosts (Crowley et al, 2009), our CSH analysis using non-vertebrate insect species did not affect the reproducibility of the hybridization data from Affymetrix GeneChips. This analysis provided insights into the first global transcriptional response of locusts to N. caninum infection.…”

Susceptibility to experimental infection of the invertebrate locusts (Schistocerca gregaria) with the apicomplexan parasiteNeospora caninum

“…This is the first study to show the benefit of CSH for an orthopteran ( S. gregaria ) species using a whole genome oligonucleotide microarray of the fruit fly Drosophila melanogaster . In line with previous studies in mammalian ( Nieto-Díaz, Pita-Thomas & Nieto-Sampedro, 2007 ) and avian hosts ( Crowley et al, 2009 ), our CSH analysis using non-vertebrate insect species did not affect the reproducibility of the hybridization data from Affymetrix GeneChips. This analysis provided insights into the first global transcriptional response of locusts to N. caninum infection.…”

Highly pathogenic avian influenza virus infection in chickens but not ducks is associated with elevated host immune and pro-inflammatory responses

“…Microarray global gene expression analysis is a useful tool to gain important insights into the effects of influenza virus infection on host gene expression that could contribute to influenza pathogenesis [ 31 ]. As commercial high density microarray platforms are not yet available for many avian species, cross species hybridization using chicken oligonucleotide microarray is a useful tool to investigate gene expression in a range of avian species [ 32 ]. In this study, we successfully demonstrated that the Chicken GeneChip array could be used for the analysis of duck transcriptome as in the previous studies with woodchuck RNA on human microarrays [ 33 ] and pig RNA on human nylon microarrays [ 31 ].…”