Great protocol; With regards to the IP of Drosophila Embryo's how many individuals did you include per replicate? Did the Qubit detect enough dsDNA with one embryo or have you included a number of embryos per replicate?
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I can see you have used ~50 mg of wet tissue/ 1000 embryos per ChIP but would still be interested to what results you generally got from the Qubit initially after sonication and then once again after IP?