Research Article

Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells

  1. Wolfgang Ernst Dr.1,*,
  2. Evelyn Trummer1,
  3. Jennifer Mead2,
  4. Conrad Bessant2,
  5. Harald Strelec3,
  6. Hermann Katinger1,
  7. Friedemann Hesse1

Article first published online: 9 MAY 2006

DOI: 10.1002/biot.200600010

Issue

Biotechnology Journal

Biotechnology Journal

Special Issue: DNA and Proteins as Diagnostic Tools

Volume 1, Issue 6, pages 639–650, June 2006

Additional Information

How to Cite

Ernst, W., Trummer, E., Mead, J., Bessant, C., Strelec, H., Katinger, H. and Hesse, F. (2006), Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells. Biotechnology Journal, 1: 639–650. doi: 10.1002/biot.200600010

Author Information

  1. 1

    Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria

  2. 2

    Department of Analytical Science and Informatics, Cranfield University at Silsoe, Silsoe, Bedfordshire, UK

  3. 3

    Institute of Applied Statistics and Computing (IASC), University of Natural Resources and Applied Life Sciences, Vienna, Austria

*Department of Biotechnology, University of Natural Resources and Applied Life Sciences, 1190 Vienna, Austria, Fax: +43-1-36006-6242

Publication History

  1. Issue published online: 14 JUN 2006
  2. Article first published online: 9 MAY 2006
  3. Manuscript Accepted: 15 MAR 2006
  4. Manuscript Revised: 9 MAR 2006
  5. Manuscript Received: 24 JAN 2006

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Keywords:

  • Chinese hamster ovary (CHO) cells;
  • Cross-species;
  • Expression signature;
  • Heat shock;
  • Oligonucleotide microarray

Abstract

Microarray technology for mammalian cells has been utilized mainly for humans, mouse, and rat gene expression analysis. In this approach the feasibility of cross-species hybridization experiments using Chinese hamster ovary (CHO) cells was evaluated. Sequence alignments of available data for CHO were performed against mouse and rat transcripts to determine the homology between the investigated species. We implemented a probability model based on this homology in order to estimate the chance for successful hybridization using Agilent's 60-mer oligonucleotide platform. Heat-shock expression data from CHO, mouse 3T3, and rat A10 cells were generated to determine intraspecies variability, reproducibility, and specificity in order to assess the accuracy of this method. Detected signature genes, in particular from studies with the mouse arrays, showed a reliable similarity between these two rodents and were confirmed by quantitative RT-PCR. Our findings provide evidence that cross-species analysis can be a useful tool to study gene expression profiles of related organisms for which species-specific microarrays are not available.

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