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MessageAmp II: Use Less RNA for Array Analysis

the amount of sample available, researchers must determine whether one or two rounds of amplification are appropriate. Microarray studies involving small samples or low mass amounts of sample RNA demand a high level of amplification (106-fold or greater). In situations like this, it is often beneficial to use the lowest level of total RNA input that generates enough cRNA for array hybridization. As little as 100 pg of total RNA can be used in the MessageAmp II procedure, and with two successive rounds of amplification, enough aRNA can often be produced for microarray analysis. Of course the amount of input RNA needed will depend on the amount of aRNA required for a particular microarray platform, and whether aRNA is also needed for replicates, follow up validation, or for archiving samples. We recommend considering two rounds of amplification when less than 100 ng of input total RNA is used.

It should be noted that the size range of aRNA produced by amplification also varies with input amount. A typical trace of the aRNA produced from 1 g and 100 ng of input RNA after 1 round of amplification is shown in Figure 2. Figure 3 shows bioanalyzer traces of aRNA produced after two rounds of amplification for several different input RNA amounts, and the bar graph in Figure 4 shows the aRNA yields for those inputs. Note that while the size of the resulting aRNA is very consistent for a given amount of total RNA input, at the very low input amounts used for two rounds of amplification, yields will vary from user to user and
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