Optimizing microarray in experimental hypertension.
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 MAS5 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.


CONCLUSIONS
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.
Shannon
M Frances
MF
John Curtin School of Medical Research, and Centre for Bioinformation Science, Australian National University, Acton, Australia.
McKenzie
Katja U S
KU
Edgley
Amanda
A
Rao
Sudha
S
Peng
Kaiman
K
Shweta
Amany
A
Schyvens
Chris G
CG
Anderson
Warwick P
WP
Wilson
Susan R
SR
Pittelkow
Yvonne E
YE
Ohms
Stephen
S
Whitworth
Judith A
JA
D000818:Animals; D018076:DNA, Complementary / Q000235:genetics; D003627:Data Interpretation, Statistical; D004195:Disease Models, Animal; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data; D006973:Hypertension / Q000209:etiology / Q000235:genetics*; D007668:Kidney / Q000378:metabolism; D008297:Male; D009392:Nephrectomy; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D051381:Rats; D017207:Rats, Sprague-Dawley
D018076:DNA, Complementary