09 September 2015 14 8K Report

I've been working on trying to get a ChIP assay to work on a protein that isn't known to be a transcription factor, but that our lab suspects acts as one in a certain disease state. My project is to induce nuclear localization of my protein of interest and then try to ChIP it and ultimately do sequencing to get an idea of where this protein is binding promoters in the genome. I've been getting low yields of DNA from my ChIPs and have been assuming failure of the protocol, but I've read many papers suggesting that ChIP DNA yield is rarely high, especially for transcription factors. The most recent ChIP assay I did gave me a concentration of 0.645 ng/uL in 50uL , so about 32ng yield, assessed by Qubit. I'm wondering whether this information alone tells me that my protocol hasn't worked, or whether I might want to consider sending the DNA out for library preparation (my university has a genomics core that will do this). I would naturally like to do qpcr, but don't have any targets to search for enrichment. Any advice would be appreciated; our lab is molecular biology, and only now incorporating -omics. 

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