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Old 02-07-2011, 03:49 AM   #20
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Originally Posted by li zhang View Post
Thx, Tonybrooks. Actually we wanna detect which genes are active during a specific period and in a particular tissue, and identify these expressed genes which are responsible for a particular physiological phenomenon. Does transcriptome sequencing work?

Could anyone answer my question about the paired-end sequencing part?
It looks like you need to do an RNA-seq experiment as you're looking for differential expression. You'll need a control sample to compare, same tissue type from a "healthy" individual. We've found transcriptome sequencing to be a very powerful tool. It's obvioulsy more sensitive than microarrays, (background is essentially zero), gives potential for identification of novel transcripts and alternative splicing events (that may not be targeted on an array), plus you have the added bonus of identifying any polymorphisms within each transcript.

We typically use paired end sequencing for RNA seq as it makes mapping much more straight-forward (although it's not essential). It basically gives us a lower number of reads that we have to throw out due to multiple mapping.
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