I'm validating my microarray data and one gene that I overexpress in my condition it's not overexpressed in the microarray output. I overexpress a short form, so maybe the affymetrix probe it's against the part of the gene that's been cut off. Just wondering if it's possible to verify that with the affymetrix probe sequence, but I can't find them anywhere.
Which species are you working with? I know how to find that information for drosophila. you can probably find that here: http://genome.ucsc.edu/cgi-bin/hgGateway
select your species,your gene and then activate in the tracks selector Affy probes.
I agree with above answers. After retrieving the annotation information including target sequence you can also include the public representative IDs. You can go with mRNA acc. no ids and designed the primer from accession no. NM_XYZ for RT-PCR experiment.
I also have a question,There are many probe sets for just one gene.how do you konw which one is suitable for your condition?and Besides,each probeset has many probes....which one to choose?
plz contact me.my e-mail:[email protected]
thx ,we have share the expriences.
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