Problem	Causes	Solution
Chromatin is under sheared and fragments are too big.	Too many cells have been used.	Reduce the number of cells.
The shearing is too low.	Increase the number of shearing cycles.
Increase the shearing peak power, the duty factor and/or the cycles/burst.
Chromatin is over sheared and fragments are too small.	Too few cells have been used.	Increase the number of cells.
The shearing is too high.	Reduce the number of shearing cycles.
Reduce the shearing peak power, the duty factor and/or the cycles/burst.
Too low recovery over IgG control and/or negative control (high background).	Not enough chromatin used for the experiment.	Increase the amount of chromatin.
Amount of antibody is too low.	Increase the amount of antibody.
Amount of antibody is too high.	Reduce the amount of antibody.
The antibody has low specificity.	Change the antibody.
Washing conditions are too stringent.	Reduce the number of washing.
Reduce the stringency of the washing buffers.
Washing conditions are not stringent enough.	Increase the number of washing.
Increase the stringency of the washing buffers.
Too much DNA was pipetted in the qPCR.	Reduce the amount of DNA pipetted in the qPCR.
qPCR conditions are not optimal.	Optimize the qPCR conditions.
Reduce the number of cycles.
No product or product is too low in the qPCR reaction of the input sample.	Not enough DNA was pipetted in the qPCR.	Increase the amount of DNA pipetted in the qPCR.
qPCR conditions are not optimal.	Optimize the qPCR conditions.
Increase the number of cycles.
Not enough chromatin used for the experiment.	Increase the amount of chromatin.
No signal in the positive control and/or panH3 ChIP.	Not enough chromatin used for the experiment.	Increase the amount of chromatin.
Amount of antibody is too low.	Increase the amount of antibody.
The antibody has low specificity.	Change the antibody.
Elution is sub-optimal.	Be sure to frequently vortex the samples to maintain the beads in solution.