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Old 08-09-2012, 06:18 AM   #1
pimento1979
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Location: Oxford UK

Join Date: Aug 2012
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Default Complete newbie- transcription factor binding sites and Deep Sequencing

Hello,

I am a PhD student and I'm looking into transgene expression using mammalian enhancer/promoter combinations. I have made variants of the enhancers, trying to pinpoint where in the sequence is responsible for expression or silencing.

My variants differ only by 70bp sequences, and so the range in which I'm looking is very tight. One of the hypotheses is that transcription factor binding sites are responsible for level and persistence of expression.

Seeing that my range is very small and standard technologies like ChiP or gel shift assays may not give me the resolution I require, I'm thinking about deep sequencing.

But like I said, I am a newbie and would appreciate any advice you experts may have on whether this is a good approach or whether I should look into something else!

Many thanks in advance for your help.
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