Microarray Sample Processing Support—Troubleshooting

Yes, high amounts of ribosomal RNA (rRNA) can influence the amplification process. Ribosomal RNAs are the most abundant types of RNA present in cells, and they can compete with messenger RNAs (mRNAs), which are usually the targets that bind to the probes on the array, during the reverse transcription and amplification steps. This competition can lead to less efficient amplification of the mRNAs, which can impact the overall quality and reliability of the outcome data.
However, it's important to note that this doesn't necessarily cause "random" primer amplification.
The primers used in these steps are designed to be specific for the mRNAs depending on the assay used and also on the probes on the array, so the presence of excess rRNA shouldn't cause them to bind and amplify random sequences. But it can reduce the efficiency with which they amplify the specific sequences for which the probes are designed for.
As a best practice, depending on the nature of the input , we often recommend that you deplete rRNA from the samples before performing these steps, especially when working with total RNA samples. There are several commercially available kits and methods for rRNA depletion.