Hello,
I am relatively new to the world of ChIPs and ChIP-seq. I am trying to prepare some samples for ChIP-seq against H3K9ac, however, my yields of ChIP DNA are low despite trying several antibodies. I am getting only about 1ng of ChIP-DNA, whereas I am told that histone ChIPs should give high yields since histone modifications are more abundant in cells. I am afraid that this might be insufficient for preparing a library of acceptable complexity. When I perform PCR using the DNA, I do see enrichment at genes of interest.
What can I do to improve yields? I use phenol chloroform extraction to purify DNA. Since I never really see the DNA pellet, maybe I am not resolublizing my ChIP-DNA in the tube completely. Would using a column purification help me get more DNA? Any suggestions would be highly appreciated. Thanks a lot!
I am relatively new to the world of ChIPs and ChIP-seq. I am trying to prepare some samples for ChIP-seq against H3K9ac, however, my yields of ChIP DNA are low despite trying several antibodies. I am getting only about 1ng of ChIP-DNA, whereas I am told that histone ChIPs should give high yields since histone modifications are more abundant in cells. I am afraid that this might be insufficient for preparing a library of acceptable complexity. When I perform PCR using the DNA, I do see enrichment at genes of interest.
What can I do to improve yields? I use phenol chloroform extraction to purify DNA. Since I never really see the DNA pellet, maybe I am not resolublizing my ChIP-DNA in the tube completely. Would using a column purification help me get more DNA? Any suggestions would be highly appreciated. Thanks a lot!
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