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

BACKGROUND: 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-de...

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Detalles Bibliográficos
Autores principales: Li, Robert W, Waldbieser, Geoffrey C
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501020/
https://www.ncbi.nlm.nih.gov/pubmed/16740160
http://dx.doi.org/10.1186/1471-2164-7-134
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author Li, Robert W
Waldbieser, Geoffrey C
author_facet Li, Robert W
Waldbieser, Geoffrey C
author_sort Li, Robert W
collection PubMed
description BACKGROUND: 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). RESULTS: 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 (R(2 )= 0.87) with the results from the microarray. CONCLUSION: 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.
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spelling pubmed-15010202006-07-13 Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus Li, Robert W Waldbieser, Geoffrey C BMC Genomics Research Article BACKGROUND: 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). RESULTS: 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 (R(2 )= 0.87) with the results from the microarray. CONCLUSION: 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. BioMed Central 2006-06-01 /pmc/articles/PMC1501020/ /pubmed/16740160 http://dx.doi.org/10.1186/1471-2164-7-134 Text en Copyright © 2006 Li and Waldbieser; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Li, Robert W
Waldbieser, Geoffrey C
Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title_full Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title_fullStr Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title_full_unstemmed Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title_short Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus
title_sort production and utilization of a high-density oligonucleotide microarray in channel catfish, ictalurus punctatus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501020/
https://www.ncbi.nlm.nih.gov/pubmed/16740160
http://dx.doi.org/10.1186/1471-2164-7-134
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