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Old 01-09-2011, 01:32 PM   #1
seqgirl123
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Default RNAi sequencing using Illumina

Does anyone sequence DNA samples that have gone through siRNA, shRNA, or miRNA screening? If yes, can someone explain how it is done on the Illumina?

Basically what I know is a typical protocol will have the siRNA/shRNA/miRNA insert in a vector or virus particle which is transfected into cells, cells go through a screening and what is left in the end are viable cells with the siRNA/shRNA/miRNA integrated into the genome. Then one wants to make sure the target gene has been silenced, so they sequence the DNA from these cells to confirm if the siRNA/shRNA/miRNA has been stably integrated into the genome and to find that it is a true match to the target gene for silencing.

But how is the sequencing aspect done on the Illumina sequencer? I have not found a good guide. Is it single-end sequencing or paired-end?
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Old 02-13-2012, 08:31 AM   #2
deo011
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No answers to this?

I have nearly the same questions. How is this analysis done?
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