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

[Steve Lianoglou]

Hi Cei,

On Nov 19, 2008, at 3:51 AM, Cei Abreu-Goodger wrote:

> Hello all,
>
> Related issues have arisen before, where the probe of a particular  
> array platform was annotated to a gene on the opposite strand. But I  
> was just asked if this even matters, or should it simply be  
> considered a case of bad probe design.
>
> Does the protocol for different manufacturer's arrays always produce  
> amplified product of both strands for the transcript to be measured?  
> I could imagine that protocols that amplify based on poly-A tails  
> would tend to produce an anti-sense biased amplification product  
> (older Affy arrays?), whereas those based on random priming could  
> produce products of both strands (and so the actual strand that is  
> on the array becomes meaningless).
>
> Does someone know what is the case in particular for Illumina  
> Beadarrays?


I've never worked on the bench-side of a microarray experiment, but  
for gene expression arrays I was under the impression that most  
protocols:

(i) extract the the RNA from cell lysate using their poly-A tails as  
targets
(ii) reverse transcribe to cDNA and amplify the cDNA w/ random primers.
(iii) hybridize amplified cDNA to the array

If that's the case, I don't think that the strand of the probe should  
be an issue.

I'd be interested, of course, to hear other people's thoughts on this,  
too (while this info should be easily available from the  
manufacturer's site, or the Methods section of many papers, let's see  
if the lazy-web can help :-).

-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos