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I have made a couple of ChIP-seq libraries using Illumina's DNA library kit. I diluted the adaptors 1:30 to compensate for much lower DNA input (10-20ng). I will be getting my sequencing data back very soon so I'll know then how good the libraries are. Since I dilute the adaptors so much I have plenty to make a bunch of libraries (not just the 10 the kit is designed for). Once I run out of the rest of the kit, I'm going to try the kits made by NEB that contain all the enzymes but not the adaptors or primers.
My question: Has any one synthesized and successfully used their own adaptors and primers? What modifications do you incorporate into the oligos? I just spoke with a rep at Illumina and they sell oligo only kits but the smallest kit they have for ChIP-seq is for 400 rxns and the cost is over $19,000!!!! It makes more sense to me to buy a DNA library prep kit for $2800 and dilute the primers. What is everyone else doing?
My question: Has any one synthesized and successfully used their own adaptors and primers? What modifications do you incorporate into the oligos? I just spoke with a rep at Illumina and they sell oligo only kits but the smallest kit they have for ChIP-seq is for 400 rxns and the cost is over $19,000!!!! It makes more sense to me to buy a DNA library prep kit for $2800 and dilute the primers. What is everyone else doing?
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