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Fig. 2.3 The hierarchy of replicates shows how complex a microarray experiment can become. It also highlights the multiple layers at which replicates are needed to ensure a microarray experiment remains valid and is not influenced by internal or external forces which are out of the scientist's control.

Because mRNA has a short half-life [29], speed of isolation through to analysis is critical. It is possible to store RNA for short periods at -80 °C without any significant degradation. Before the RNA is used for further analysis it is essential to DNAse-treat the sample. This is to ensure the preparation is pure, as RNA extraction protocols often isolate genomic DNA at the same time, which would give a false positive signal in an array experiment. In some cases researchers have removed ribosomal RNA (rRNA), but we find this inconsistent and unnecessary for bacteria. As an added benefit, many arrays contain probes against rRNA so that it can be used as a positive control, or even as a normalization factor.

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