ATAC-seq generally requires high levels of cell viability. Previous experiences in my lab show that in my cell line, 6uM of cisplatin for 8h leads to a larger p53 response (there is a smaller but noticeable response after 4h). I would Like to do ATAC-seq in samples where I induce DNA damage in this condition, but I am concerned that inducing the DNA damage will reduce cell viability at the time of collection. Ive read that some researchers treat their cells with 200U/ml DNase for 30min at 37C (and double washing with PBS) before collecting cells so that the DNA of dead and free-floating cells would be digested. Does this work?
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