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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR ANALYSIS OF SALMONELLA VIRULENCE, ANTIBIOTIC RESISTANCE, AND HOST RESPONSE Title: Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays

Authors
item Tuggle, Christopher -
item Bearson, Shawn
item Uthe, Jolita -
item Huang, T -
item Qu, Long -
item Couture, Oliver -
item Wang, Yanfang -
item Kuhar, Daniel
item Lunney, Joan
item Nettleton, Dan -
item Honavar, Vasant -
item Dekkers, Jack -

Submitted to: Veterinary Immunology and Immunopathology
Publication Type: Review Article
Publication Acceptance Date: June 9, 2010
Publication Date: December 15, 2010
Citation: Tuggle, C.K., Bearson, S.M., Uthe, J.J., Huang, T.H., Qu, L., Couture, O.P., Wang, Y., Kuhar, D.J., Lunney, J.K., Nettleton, D., Honavar, V., Dekkers, J.C. 2010. Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays. Veterinary Immunology and Immunopathology. 138(4):280-291.

Interpretive Summary: This review addresses technological developments in both the collection and analysis of molecular genetic data for transcriptomics (gene expression analyses). Over the past few years numerous options for exploring and improving our understanding of the global response to immune stimulants and infectious pathogens have become available. These developments are particularly dramatic for scientists studying the pig, where tools are now available to measure the expression of tens of thousands of gene transcripts, as well as the updated porcine genome sequence. These have combined to expand our abilities to elucidate the porcine immune system and the cell, tissue and whole pig response to infections. In this review, we describe these recent developments in the context of our work exploring gene expression changes during infection of pigs by Salmonella. This is not a comprehensive review of all possible approaches, our goal is to provide links and information on the tools for gene expression/transcriptomic analyses, alternative approaches for transcriptomic data collection and best methods for statistical analysis of the resultant data and its impact for porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests.

Technical Abstract: Technological developments in both the collection and analysis of molecular genetic data over the past few years have provided new opportunities for an improved understanding of the global response to pathogen exposure. Such developments are particularly dramatic for scientists studying the pig, where tools to measure the expression of tens of thousands of transcripts, as well as unprecedented data on the porcine genome sequence, have combined to expand our abilities to elucidate the porcine immune system. In this review, we describe these recent developments in the context of our work exploring gene expression changes during infection of pigs by Salmonella. Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data collection and analysis of porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests.

Last Modified: 10/31/2014
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