Intercenter reliability and validity of the rhesus macaque GeneChip

Fenghai Duan, Eliot R. Spindel, Yu Hua Li, Robert B Norgren

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Background: The non-human primate (NHP) research community has been intensely interested in obtaining whole-genome expression arrays for their work. Recently, novel approaches were used to generate the DNA sequence information for a rhesus GeneChip. To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources: cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line. Aliquots of this RNA were sent to each of three centers: Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center. Each center labeled the samples and hybridized them with two rhesus macaque GeneChips. In addition, rhesus samples were hybridzed with human GeneChips to compare with samples hybridized with the rhesus GeneChip. Results: The results indicate that center effects were minimal and the rhesus GeneChip appears highly reliable. To test the validity of the rhesus GeneChip, five of the most differentially expressed genes among tissues identified in the reliability experiments were chosen for analysis with Quantitative PCR. For all 5 genes, the qPCR and GeneChip results were in agreement with regard to differential expression between tissues. Significantly more probesets were called present when rhesus samples were hybridized with the rhesus GeneChip than when these same samples were hybridized with a human GeneChip. Conclusion: The rhesus GeneChip is both a reliable and a valid tool for examining gene expression and represents a significant improvement over the use of the human GeneChip for rhesus macaque gene expression studies.

Original languageEnglish (US)
Article number61
JournalBMC genomics
Volume8
DOIs
StatePublished - Mar 19 2007

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Macaca mulatta
Reproducibility of Results
Primates
Research
RNA
Gene Expression
Cerebral Cortex
Thymus Gland
Genes
Testis
Pancreas
Fibroblasts
Genome
Cell Line
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Intercenter reliability and validity of the rhesus macaque GeneChip. / Duan, Fenghai; Spindel, Eliot R.; Li, Yu Hua; Norgren, Robert B.

In: BMC genomics, Vol. 8, 61, 19.03.2007.

Research output: Contribution to journalArticle

Duan, Fenghai ; Spindel, Eliot R. ; Li, Yu Hua ; Norgren, Robert B. / Intercenter reliability and validity of the rhesus macaque GeneChip. In: BMC genomics. 2007 ; Vol. 8.
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