What factors should I consider when performing single-sample probe sonication for my ChIP experiment?

There are various factors to consider when  performing single-sample probe sonication for ChIP experiments. 

• The probe must be directly inserted into the tube for direct sonication. 
• Chromatin is processed with a buffer containing SDS (0.1%-10%), along with protease inhibitors to enhance sonication efficiency, epitope availability, and chromatin yield. 
• Proper positioning of the probe (so it doesn't make contact with the tube side) is crucial to ensure consistent chromatin shearing between samples. 
• Careful cleaning of the probe between samples is essential to prevent cross-contamination. 
• To prevent overheating during sonication, samples must be kept cold. While ice can be used, it may not maintain a constant low temperature, especially when processing multiple samples. A cooling instrument ensures consistent temperature throughout the sonication process and between samples. 
• Sonication time or amplitude may need to be increased for efficient sonication if nuclei are not isolated or chromatin is highly compacted. Conversely, sonication time or amplitude should be decreased in order if the target protein is experiencing degradation.