Hey guys,
I've a question regarding the size selection step in the generation of an illumina library for ChIP-Seq. The particular cells I'm using are especially difficult to sonicate, hence my DNA fragments are approx. 200-1000+ base pairs at the input stage of my ChIP. This means that the normal size selection step would only get a small fraction of my DNA. The average size of my fragments is approx. 500 base pairs and I'd prefer to extend the size selection up the gel a bit to get as much of my DNA as possible. What is the maximum size of fragment that can be efficiently used for library generation? Ideally I'd like also to take a wider size range, say from 350-800 because my fragment smears are relatively diffuse compared to other sonications. Is it possible to do this?
Cheers
Optimus
I've a question regarding the size selection step in the generation of an illumina library for ChIP-Seq. The particular cells I'm using are especially difficult to sonicate, hence my DNA fragments are approx. 200-1000+ base pairs at the input stage of my ChIP. This means that the normal size selection step would only get a small fraction of my DNA. The average size of my fragments is approx. 500 base pairs and I'd prefer to extend the size selection up the gel a bit to get as much of my DNA as possible. What is the maximum size of fragment that can be efficiently used for library generation? Ideally I'd like also to take a wider size range, say from 350-800 because my fragment smears are relatively diffuse compared to other sonications. Is it possible to do this?
Cheers
Optimus
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