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Hi all
I'm new to ChIP so I'm looking for some advice.
We've sheared our DNA and QC'd and it looks to be roughly the correct size (see Bioanalyser). However, when we do the IP, we seem to lose everything >100bp and are left with one large peak around 90bp (again, on the trace), plus something below baseline immediately after. No idea what causes the negative peak.
Are there any tips on how we can improve our ChIP technique so we have larger material available to make a library from? Alternatively, can anyone recommend a protocol for generating a library from these small DNA fragments. We have tried a couple of times to prep a library, but I think I'm losing the product after each clean up step because it's so small.
Thanks in advance
I'm new to ChIP so I'm looking for some advice.
We've sheared our DNA and QC'd and it looks to be roughly the correct size (see Bioanalyser). However, when we do the IP, we seem to lose everything >100bp and are left with one large peak around 90bp (again, on the trace), plus something below baseline immediately after. No idea what causes the negative peak.
Are there any tips on how we can improve our ChIP technique so we have larger material available to make a library from? Alternatively, can anyone recommend a protocol for generating a library from these small DNA fragments. We have tried a couple of times to prep a library, but I think I'm losing the product after each clean up step because it's so small.
Thanks in advance