Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations

J. D. Chismar, T. Mondala, H. S. Fox, E. Roberts, D. Langford, E. Masliah, D. R. Salomon, S. R. Head

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

There exists a significant limitation in the variety of organisms for which microarrays have been developed because of a lack of genomic sequence data. A near-term solution to this limitation is to use microarrays designed for one species to analyze RNA samples from closely related species. The assumption is that conservation of gene sequences between species will be sufficient to generate a reasonable amount of good-quality data. While there have been relatively few published reports describing the use of microarrays for cross-species hybridizations, this technique is potentially a powerful tool for understanding genomics in model organisms such as nonhuman primates. Here we describe the analysis and comparison of hybridization characteristics and data variability from a set of crossspecies (rhesus macaque) and same-species (human) hybridization experiments using human high-density Affymetrix oligonucleotide arrays, The data reveal that a large fraction of probe sets are effective at transcript detection in the cross-species hybridization, validating the application of cross-species hybridizations for nonhuman primate genomics research.

Original languageEnglish (US)
Pages (from-to)516-524
Number of pages9
JournalBioTechniques
Volume33
Issue number3
StatePublished - Sep 1 2002

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Microarrays
Genomics
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Primates
Macaca mulatta
RNA
Conservation
Genes
Research
Experiments
Data Accuracy

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Chismar, J. D., Mondala, T., Fox, H. S., Roberts, E., Langford, D., Masliah, E., ... Head, S. R. (2002). Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. BioTechniques, 33(3), 516-524.

Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. / Chismar, J. D.; Mondala, T.; Fox, H. S.; Roberts, E.; Langford, D.; Masliah, E.; Salomon, D. R.; Head, S. R.

In: BioTechniques, Vol. 33, No. 3, 01.09.2002, p. 516-524.

Research output: Contribution to journalArticle

Chismar, JD, Mondala, T, Fox, HS, Roberts, E, Langford, D, Masliah, E, Salomon, DR & Head, SR 2002, 'Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations', BioTechniques, vol. 33, no. 3, pp. 516-524.
Chismar, J. D. ; Mondala, T. ; Fox, H. S. ; Roberts, E. ; Langford, D. ; Masliah, E. ; Salomon, D. R. ; Head, S. R. / Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. In: BioTechniques. 2002 ; Vol. 33, No. 3. pp. 516-524.
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