Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells.
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.
Ernst
Wolfgang
W
Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria. w.ernst@iam.boku.ac.at
Trummer
Evelyn
E
Mead
Jennifer
J
Bessant
Conrad
C
Strelec
Harald
H
Katinger
Hermann
H
Hesse
Friedemann
F
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D016466:CHO Cells; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D006224:Cricetinae; D003412:Cricetulus; D020869:Gene Expression Profiling / Q000379:methods*; D051379:Mice; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D051381:Rats; D011994:Recombinant Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics*
D011994:Recombinant Proteins; D014157:Transcription Factors