Chip-seq blocking reagent - Samlon 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!

Monica

You could try using tRNA instead. You might have to optimize the concentration but a good place to start is 200µg/ml. A colleague of mine did a side-by-side comparison with 200µg/ml sheared salmon sperm DNA and the results were identical.