Shannon M Frances, McKenzie Katja U S, Edgley Amanda, Rao Sudha, Peng Kaiman, Shweta Amany, Schyvens Chris G, Anderson Warwick P, Wilson Susan R, Pittelkow Yvonne E, Ohms Stephen, Whitworth Judith A
John Curtin School of Medical Research, and Centre for Bioinformation Science, Australian National University, Acton, Australia.
Kidney Int. 2005 Jan;67(1):364-70. doi: 10.1111/j.1523-1755.2005.00090.x.
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.
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.
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.
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.
远交动物之间的基因噪声可能是在使用微阵列技术进行基因表达谱分析时的一个主要混杂因素。对同一动物的配对器官进行研究提供了一种替代方法（例如，用于实验性高血压中肾脏的研究）。本研究旨在确定远交成年Sprague-Dawley（SD）大鼠之间的基因噪声水平，并确定单侧肾切除对基因表达变化的影响，以此作为实验性高血压微阵列研究设计的基础。
雄性SD大鼠（约130克）在测量尾袖收缩压（SBP）前进行适应性饲养，共6天对照期和4天生理盐水处理期。进行左肾切除术，将组织在液氮中速冻以备后续RNA提取。两周后，在4天对照期和8天生理盐水处理期测量SBP，然后切除并冷冻剩余的右肾。进行总RNA纯化、cRNA制备、杂交以及对Affymetrix Rat U34A阵列进行扫描，并使用Affymetrix Suite（v5）的MAS5软件、Bioconductor以及相关模拟激发的统计方法对数据进行分析。
不同动物的左对照肾中的基因表达谱极为一致。然而，同一动物的配对肾的表达谱比不同动物的肾的表达谱更为相似。在研究的时间范围内，肾切除对基因表达谱影响很小。
尽管本研究中使用的大鼠是远交的，但它们可用于基因表达谱比较。使用单个动物的配对器官可确保更高的基因一致性，从而能够确定受感兴趣的处理影响而发生改变的基因。
