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I do not think your library prep has worked.
Running these on a high-sensititvity kit will give you more confidence that they have not so it is probably still worth it for peace of mind.
Did you read the Sanger paper from 2008? This has lots of tips for improving library prep. Most of all for ChIPseq you need to titrate the adapters against input DNA, many of my users are using 50x lower adapter concentration.
Use teh gel picking tips from Cleaver Scientific or elsewhere to make sure you only get your band of interest into the final PCR. Gel purify before PCR but also cut bands (with new tips) at above and below your region of interst. If the PCR goes wrong then you have a sample to repeat it from, albeit at a different size.
Forget the nanodrop! Illumina have a QPCR protocol now try that.
Good luck.
Running these on a high-sensititvity kit will give you more confidence that they have not so it is probably still worth it for peace of mind.
Did you read the Sanger paper from 2008? This has lots of tips for improving library prep. Most of all for ChIPseq you need to titrate the adapters against input DNA, many of my users are using 50x lower adapter concentration.
Use teh gel picking tips from Cleaver Scientific or elsewhere to make sure you only get your band of interest into the final PCR. Gel purify before PCR but also cut bands (with new tips) at above and below your region of interst. If the PCR goes wrong then you have a sample to repeat it from, albeit at a different size.
Forget the nanodrop! Illumina have a QPCR protocol now try that.
Good luck.
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