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First published online April 20, 2007
Journal of Experimental Biology 210, 1602-1606 (2007)
Published by The Company of Biologists 2007
doi: 10.1242/jeb.002402
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Comparative environmental genomics in non-model species: using heterologous hybridization to DNA-based microarrays

Bradley A. Buckley

Department of Biology, Portland State University, Portland, OR 97201, USA


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  		Fig. 1. Two general experimental designs often employed by studies using heterologous hybridization to microarrays. In the first design (A), samples from two different species (species 2 and 3) are competitively hybridized against one another to a microarray generated from oligonucleotides or cDNAs from a single species (species 1). Note that, in some cases, species 1 may be the same as either 2 or 3. In this design, the sequence distance between species 1 and 2 will differ, to some degree, from that between 1 and 3; if this difference is too great, it may affect hybridization kinetics, which may in turn artificially affect the generated gene expression values. Under the second design (B), the two hybridized samples are always from the same species, and the two samples generally differ in another variable, e.g. treatment, time point or tissue. With this design, the only sequence divergence factor is that between species 1 and 2, and this factor should affect both hybridized samples equally.

 

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© The Company of Biologists Ltd 2007