Optimizing microarray in experimental hypertension

M. Frances Shannon, Katja U.S. McKenzie, Amanda Edgley, Sudha Rao, Kaiman Peng, Amany Shweta, Chris G. Schyvens, Warwick P. Anderson, Susan K. Wilson, Yvonne E. Pittelkow, Stephen Ohms, Judith A. Whitworth*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    3 Citations (Scopus)

    Abstract

    Background. Genetic noise between outbred animals can potentially be a major confounder in the use of microarray technology for gene expression profiling. The study of paired organs from the same animal offers an alternative approach (e.g., for studies of the kidney in experimental hypertension). The present study was undertaken to determine the level of genetic noise between outbred adult Sprague-Dawley (SD) rats, and to determine the effects of unilateral nephrectomy on changes in gene expression as a basis for the design of microarray studies in experimental hypertension. Methods. Male SD rats (approximately 130 g) were acclimatized before measurement of tail-cuff systolic blood pressure (SBP) for 6 control days and 4 days of saline treatment. Left kidney nephrectomy was performed, and the tissue snap-frozen in liquid nitrogen for subsequent RNA extraction. Two weeks later, SBP was measured over 4 control and 8 saline treatment days, and the remaining right kidney removed and frozen. Total RNA purification, preparation of cRNA, hybridization, and scanning of the Rat U34A Affymetrix arrays were performed, and data analyzed using MASS software Affymetrix Suite (v5), Bioconductor, as well as statistical methods motivated by relevant simulations. Results. Gene expression profiles in the left control kidney were extremely consistent across animals. The expression profiles of pairs of kidneys from the same animal were, however, more similar than those of kidneys from different animals. Nephrectomy had little effect on the gene expression profiles in the time frame examined. Conclusion. Despite the outbred nature of the rats used in this study, they are useful for gene expression profiling comparisons. The use of paired organs from an individual animal ensures even further genetic identity, allowing determination of genes modified by the treatment of interest.

    Original languageEnglish
    Pages (from-to)364-370
    Number of pages7
    JournalKidney International
    Volume67
    Issue number1
    DOIs
    Publication statusPublished - Jan 2005

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