Assessment of the swine protein-annotated oligonucleotide microarray

  1. J. P. Steibel1,2,
  2. M. Wysocki3,
  3. J. K. Lunney3,
  4. A. M. Ramos1,†,
  5. Z.-L. Hu4,
  6. M. F. Rothschild4,
  7. C. W. Ernst1

Article first published online: 8 JUN 2009

DOI: 10.1111/j.1365-2052.2009.01928.x

Issue

Animal Genetics

Animal Genetics

Volume 40, Issue 6, pages 883–893, December 2009

Additional Information

How to Cite

Steibel, J. P., Wysocki, M., Lunney, J. K., Ramos, A. M., Hu, Z.-L., Rothschild, M. F. and Ernst, C. W. (2009), Assessment of the swine protein-annotated oligonucleotide microarray. Animal Genetics, 40: 883–893. doi: 10.1111/j.1365-2052.2009.01928.x

Author Information

  1. 1

    Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA

  2. 2

    Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA

  3. 3

    Animal Parasitic Diseases Laboratory, ANRI, BARC, ARS, USDA, Beltsville, MD 20705, USA

  4. 4

    Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA

  1. †

    Present address: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.

*J. P. Steibel, Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA. E-mail: steibelj@msu.edu

  • †

    Present address: Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands.

Publication History

  1. Issue published online: 6 NOV 2009
  2. Article first published online: 8 JUN 2009
  3. Accepted for publication 21 April 2009

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Keywords:

  • amplified antisense RNA;
  • long oligo array;
  • pig;
  • quantitative PCR

Summary

The specificity and utility of the swine protein-annotated oligonucleotide microarray, or Pigoligoarray (http://www.pigoligoarray.org), has been evaluated by profiling the expression of transcripts from four porcine tissues. Tools for comparative analyses of expression on the Pigoligoarray were developed including HGNC identities and comparative mapping alignments with human orthologs. Hybridization results based on the Pigoligoarray’s sets of control, perfect match (PM) and deliberate mismatch (MM) probes provide an important means of assessing non-specific hybridization. Simple descriptive diagnostic analyses of PM/MM probe sets are introduced in this paper as useful tools for detecting non-specific hybridization. Samples of RNA from liver, brain stem, longissimus dorsi muscle and uterine endothelium from four pigs were prepared and hybridized to the arrays. Of the total 20 400 oligonucleotides on the Pigoligoarray, 12 429 transcripts were putatively differentially expressed (DE). Analyses for tissue-specific expression [over-expressed in one tissue with respect to all the remaining three tissues (q < 0.01)] identified 958 DE transcripts in liver, 726 in muscle, 286 in uterine endothelium and 1027 in brain stem. These hybridization results were confirmed by quantitative PCR (QPCR) expression patterns for a subset of genes after affirming that cDNA and amplified antisense RNA (aRNA) exhibited similar QPCR results. Comparison to human ortholog expression confirmed the value of this array for experiments of both agricultural importance and for tests using pigs as a biomedical model for human disease.

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