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Open Access Research article

Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus

Robert W Li12 and Geoffrey C Waldbieser1*

Author Affiliations

1 USDA, Agricultural Research Service, Catfish Genetics Research Unit, Stoneville, MS 38776, USA

2 USDA, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA

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BMC Genomics 2006, 7:134  doi:10.1186/1471-2164-7-134

Published: 1 June 2006



Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide microarray platform based on channel catfish EST sequences. This platform was used to profile gene expression in catfish spleens 2 h, 4 h, 8 h and 24 h after injection of lipopolysaccharide (LPS).


In the spleen samples, 138 genes were significantly induced or repressed greater than 2-fold by LPS treatment. Real-time RT-PCR was used to verify the microarray results for nine selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R2 = 0.87) with the results from the microarray.


The first generation channel catfish microarray provided several candidate genes useful for further evaluation of immune response mechanisms in this species. This research will help us to better understand recognition of LPS by host cells and the LPS-signalling pathway in fish.