Hi,

I am working towards standardizing and performing ChIP-Seq experiments on Arabidopsis thaliana seedlings and roots. The mutant line I am using is tagged to YFP. I use about 1g of plant material. Do a formaldehyde fixation (10 minutes under vacuum and 10 minutes without vacuum). I shear the DNA using a Bioruptor Plus (from Diagenode) – 30 seconds shearing – 60 seconds stop and 30 cycles. I get fragment size between 300bp to 1500bp. I do an IP with GFP antibody from abcam and Protein G dyna beads from Invitrogen. I use 10-20 ug of DNA for IP. After IP I do DNA purification using Qiagen Min-elute DNA purification kit. I end up with very low concentration (2-10ng/ul in a 10 ul elution with elution buffer) and low A260/230 values (between 0.5-1.5).

I had two concerns regarding this

How can I increase the shearing efficiency (to get sheared DNA between 200bp-500bp)?

How can I increase the concentration of the DNA after IP?

Any suggestions will be appreciated. Thank you