i am having a problem with chip assays following sonication with bioruptor.
i have done the same chip assays successfully before but i was sonicating with probe sonicator.
Since now i have to prepare the samples for chipseq, we have got bioruptor 400 in our lab along with water bath to mintain temp at 4 degrees.
i am using 15 cycles (30sec on 30 sec off) with bioruptor and exactly same fixation and chip protocol as i have used before with mouse cortex and pol2 antibodies. I am using millipore ez magna chip kit (cat no-17-409).
So the only difference now is sonicating with bioruptor (fragments of 100-600bp)instead of probe sonicator and my chipqpcr does not work even with the positive control primers (b-tubulin, pcr product size 100bp).
please help me solve this issue.
Thanks very much...
i have enclosed my chip-protocol