[BioC] Does the strand of a microarray probe matter?

[Maria Stalteri]

Hi Cei,

The Illumina BeadArrays use a variety of assays. 

The whole genome gene expression arrays such as the HumanWG-6 and 
HumanRef-8 use a 3' based 
assay (IVT or in-vitro transcription assay) very similar to the one used 
with the older 3' Affymetrix arrays. 

Some of the older or custom gene expression arrays which use Illumina's 
universal BeadChips use the DASL assay, which uses a combination of 
poly(T) priming and random priming.


However, if we are talking about gene expression arrays, both types of 
protocol start with an RNA sample, so they will only amplify transcripts
that are expressed, whichever strand they are transcribed from.


The problem with probes on the wrong strand is that you will not be able 
to detect expression from the gene in question if the probe is on the 
opposite strand. If a probe that is on the wrong strand gives a signal 
that indicates expression, then what is really being expressed is possibly 
an antisense transcript which may have some regulatory function.

Best wishes,
Maria