It is important to minimize variance/noise inherited from different biological samples and technical procedures because microarray technology is extremely sensitive to these variances. One common solution is to perform "RNA sample pooling". In this process, 2 or more RNA samples isolated from individual, parallel experiments are pooled prior to cRNA synthesis and hybridization to a GeneChip. RNA pooling generally minimizes variances caused by individual subject difference (ex. mouse A to mouse B) and technical difference (ex. different ways of sample handling on different days). However, a drawback of performing RNA pooling is that it may obscure subtle changes of gene expression in a low-replicate experiment. Also, if differences among individual subjects are of your interest, RNA pooling should NOT be applied. For example, RNA pooling of two different mice would obscure circadian rhythm, which is unique to an individual mouse. For more detail, please refer to the microarray related papers listed on our website.
A well thought experimental design is a good start and RNA quality is critical when it comes to microarray experiments. Pure, intact RNA is a prerequisite for good array results. Fresh reagents and meticulous techniques can also make a large difference between good targets and no targets. Therefore, it is critical to work with a highly reputable DNA core facility. Last but not the least, appropriate statistical analysis is a critical factor for the meaningful interpretations of microarray results.
Please visit Affymetrix for questions related to GeneChip or contact us for further assistance.
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