Hi,
Based on results from ChIP-Seq experiments I chose ~10-15 potential chromatin interactions in different loci in the genome which I want to check.
Does anyone a suggestion which approach will be the best to check them? Should I choose a method which is followed by PCR or sequencinq, which one will be better time- and cost-wise to check these 10-15 interactions?
Thank you for any help!
Hello,
You could try a 3C (Chromosome Conformation Capture) assay based on the fact that you have prior insights into the potential interractions through ChIP assay. Your readout will be qPCR data. It‘s less labor intensive in terms of processing your samples and your data afterward. And that sounds the logical way to go based on what you stated. You can choose between a 3C after cross linking or a native 3C to account for potential artifacts due to cross linking.
But if your budget permits, you could opt for a 4C assay instead. Your readout will be sequencing data instead of qPCR as in the 3C assay. It is obviously more labor intensive and costly. You might come across new interactions you missed with your ChIP-qPCR assay.
Good luck
I completely agree with Vincent Yapo. Please go through the attach review article for your better understanding.
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