On Jan 7, 2008 8:45 AM, Marie-Paule Roth <roth@cict.fr> wrote:

> Dear All,
> Our goal is to localize eQTLs in both the liver and the spleen, using
> 200 F2 mice. We thus need to measure gene expression levels in the
> two organs of 200 mice. We are using Agilent 4x44K arrays. For cost
> reasons, I was planning to label liver mRNAs with Cy3 and spleen
> mRNAs with Cy5, hybridize the 2 mRNAs of the same mouse on one array,
> and analyse liver and spleen data separately (eQTLs can differ in
> both organs). Of course, we expect gene expression variability
> between F2 mice, at least for a significant proportion of genes. Is
> there a chance that high gene expression in one organ can influence
> the detected level of fluorescence in the other organ and thus bias
> the results ? If so, is there a way to deal with this problem ?
>

We have done this sort of thing using Agilent Tiling arrays and have not
seen a significant problem with that approach.

Sean

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