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Hi,
I am doing ATAC-seq on sorted lymphocytes, but I find that I always need more than the recommended 6 extra PCR cycles (11 total) to reach one third maximal fluorescence on the qPCR, even with 100,000 cells. I think that I am probably losing cells/material during the wash steps. I was wondering whether anyone has any tips for removing the supernatant without dislodging the pellet too much? I am making sure to remove the supernatant from the opposite side of the eppendorf to the pellet. Also, I have a question regarding FBS. Is it ok to sort into media containing FBS, as someone else mentioned in a post that their library was contaminated with bovine DNA?
Thanks for any advice!
I am doing ATAC-seq on sorted lymphocytes, but I find that I always need more than the recommended 6 extra PCR cycles (11 total) to reach one third maximal fluorescence on the qPCR, even with 100,000 cells. I think that I am probably losing cells/material during the wash steps. I was wondering whether anyone has any tips for removing the supernatant without dislodging the pellet too much? I am making sure to remove the supernatant from the opposite side of the eppendorf to the pellet. Also, I have a question regarding FBS. Is it ok to sort into media containing FBS, as someone else mentioned in a post that their library was contaminated with bovine DNA?
Thanks for any advice!
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