Hi all, I am trying to sonicate 4T1 breast cancer cells to perform ChIP-sequencing. My first question is, what would be the best procedure to check ChIP sonication efficiency on agarose gel?
My current protocol:
Take 50uL from sonicated sample, add 150uL ChIP elution buffer
Reverse crosslink overnight on 65 degrees
Add 1uL of 20mg/mL proteinase K, leave on 42 degrees for one hour
Extract DNA using DNA extraction column
Add 1uL of 20mg/mL RNase A, leave on 37 degrees for 30 mins
Add loading buffer and water, run on agarose gel
The agarose gel picture is attached below, I don't really understand why in some lanes, there are two smears (one around 500bp, one above 1000bp)
Would be really helpful If someone has sonication recommendation for 4T1 cells as well. My lab owns a single probe sonicator.
Thank you so much! All advices are welcomed!
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