In my lab we did a microarray to analyze differential gene expression in S. cere

Question

In my lab we did a microarray to analyze differential gene expression in S. cerevisiae treated with UV irradiation. We are now analyzing the results and one of the up-regulated genes is labeled "Alien4_60." I believe this is some kind of control, but I am having trouble understanding what it is.

I would think that a probe labeled "alien" in a microarray would be some kind of negative control. The probe-list (excel file) says "Control stringency: 60% identity to oligo Alien4" as the description for this probe. What does this mean?

Explanation / Answer

It's a probe to detect external 'Alien' RNA standard, a synthetic mRNA commercialized by Stratagene/Agilent.

The Alien RNA transcript is a ~500-nt, polyadenylated RNA molecule that is synthesized by in vitro transcription. The Alien RNA transcript is nonhomologous to all known nucleic acid sequences currently in public databases, as determined by BLAST comparisons against NIH sequence databases.

As any other external standard, you spike in the same amount of Alien RNA standard in your different reactions and then using the Alien probe you can normalize for extraction efficiencies etc. It works not only for microarrays, but also for qPCR, RNA-seq etc.

If you didn't spike in any of it, I expect your probes giving very low signal that's probably why you thought about negative controls.

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