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Chip-seq blocking reagent - Salmon DNA is useful for Chip-chip (Nov/11/2010 )

I am working with ChIP Sequencing now. Since I used our protocol for Chip-chip before, we add BSA and Salmon DNA together to the magnetic beads, which help us to get lower background. But I couldn't use Salmon DNA for ChIP Sequencing, these DNA will be sequenced.
But our Chip-seq data isn't good since the background is so noisy and the peaks is too lower.

Does anybody use some other reagents to block unsepecific DNA when work with Chip?

Thank you!



You definitely need to avoid using any DNA carrier such as salmon sperm DNA, calf thymus DNA as blocking reagents. To minimize nonspecific binding, magnetic beads (Dynabeads) should be used because they do not readily absorb random DNA as sepharose.