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Perform Microarray Analysis with Limited Bacterial RNA

all technical replicate comparisons was >0.995. The sensitivity (% Present Calls) obtained with MessageAmp II-Bacteria is comparable to the standard Affymetrix labeling protocol, as is the call concordance between replicates. (See article in previous issue for a more complete definition of sensitivity and concordance analysis.) Thus, MessageAmp II-Bacteria enables you to use significantly less starting material without compromising the quality of microarray data.

Figure 3. Affymetrix E. coli Antisense Genome Array Replicate Analysis. Scatter plots of log signal for replicate labeling reactions using Affymetrix E. coli antisense whole genome arrays (all 7312 probe sets are shown). Either E. coli total RNA or enriched mRNA derived from it (MICROBExpress Kit) was used with the recommended Affymetrix labeling protocol or Ambions MessageAmp II-Bacteria biotin IVT labeling protocol. The data was analyzed with Affymetrix Microarray Suite, Version 5 with scaling to all probe sets and a target signal value of 500. 2, 3, 10 and 30-fold change lines are represented.


Tips for Bacterial RNA Amplification
When using MessageAmp II-Bacteria for expression analysis, Ambion recommends that the researcher use similar input RNA mass amounts, RNA type (total RNA or mRNA), and IVT incubation times when performing comparisons between samples. Also, as with other RNA amplification methods, only amplified samples should be compared to one another. Unamplified samples should
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