I have completed my cross-species microarray experiments on a 70-mer oligo slide for Giardia lamblia. I ran the GS and WB isolates on a WB isolate microarray. The two isolates have been recently sequenced. I know a lot of my down-regulated genes in the GS isolate are the result of mismatches in the WB probe for the GS mRNA. I was wondering how I would determine what down-regulated genes are reliable and which ones are due to mismatches? I have the sequences of both isolates to compare. If you know of any papers that have done similar cross species experiments with two sequenced species that would be extra helpful.
Second, my supervisor thinks I should be using a equation to estimate the hybridization temperature of the mismatched cDNA to the probe. I was wondering if anyone knew of some free software that can do these calculations.
Cross species hybridization-How do I deal with down regulated genes caused by micross species mismatch
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