I am planning to detect antisense transcripts for some of the selected genes for which antisense transcripts have been detected by the strand specific microarray experiments conducted by me. Can anyone suggest the best protocols to use to conduct strand specific realtime/RT pcr to validate my findings. The experiment is focused on detecting antisense transcripts from the protozoan parasite Plamsodium falciparum.
These articles should answer ur query, though for viral RNA
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007468
http://www.ncbi.nlm.nih.gov/pubmed/16199097
http://www.biomedcentral.com/1471-2199/12/3
and, this one would help u in assessment too :
http://genomebiology.com/content/11/8/R87
Best one would be to tag the primer (simplest Biotin tag) and southern blot the transcripts or PCR pdts.
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