I'm planning a microarray experiment using a genome from a bacterium that is not amenable to genetic manipulation. However I do have another strain of the same bacterium that I can make mutations in but that has not been sequenced. My question: 1) should I set up the microarray experiment using the sequenced strain and make mutations in interesting genes in the second strain. My problem with this is if I find a regulatory gene, I will not be able to use the microarray to determine the genes in the regulatory pathway 2) should I use the microarray to do comparitive genomic analysis to determine genomic differences. My problem with this is that even small difference (~10%) may result in a difference of ~200 genes. I've been having trouble finding what may be acceptable in the literature.