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Support | FAQs | Bioruptor® | Problem with the optimization of conditions

Problem with the optimization of sonication conditions

Dear Bioruptor User,

The Bioruptor can be used for many different applications. For each application and experimental conditions the sonication conditions have to be optimized.

If you start to use the Bioruptor, the results of sonication are not good and you need our help, please, answer to the questions attached below (PROBLEM WITH THE SONICATION OPTIMIZATION) and send them to support@diagenode.com

General questions

1. Which model of Bioruptor do you use? UCD-200 (Bioruptor®)
UCD-300 (Bioruptor® Next Gen)
UCD-400 (Bioruptor® Twin)
XL-2600 (Bioruptor® XL)

2. How do you control the temperature during the sonication? using cooling system
using crushed ice (inside of cold room)
using crushed ice (outside of cold room)

3A. If you use the cooling system, what is the speed of water flow? 3B. If you use the crushed ice, how much of it do you use? 4. Do you squeeze breaks in the run when you sonicate a longer time? 5. What is the level of the water in the tank during the sonication?

Questions about the protocol which you use

6. Which cells do you use? 7. What fixation agent(s) do you use? 8. What is the final concentration of fixation agent(s) which you use? 9. How long and in which temperature do you fix the samples? 10. How do you stop the fixation (what do you use, time, concentration)? 11. What cell lysis buffer do you use? 12. What is the concentration of cells in the cell lysis buffer? 13. Which detergent and in which final concentration do you include in the shearing buffer? 14. What is the amount of cells in the shearing buffer and the volume of the sample? 15. What is the total time of sonication? 16. How long the cycles are (time “ON” and “OFF” of the sonication)? 17. What is the power setting which you use (low, medium, high)? 18. What is the size of tube you use? Which brand? 19. What volume of sample do you use in the tube? 20. If you use the tubes bigger the 1,5ml do you use our reflecting bars? 21. How many tubes do you sonicate simultaneously? 22. What is the size of the chromatin/DNA fragments after shearing? Any additional comments? :

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