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Old 01-27-2017, 08:49 AM   #1
lc16
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Location: US

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Default ATAC-seq - cell/material loss during wash steps

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!
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Old 08-20-2017, 11:30 PM   #2
Adriana Cantoran
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Hi! I am having the same issue, with same cell type. Did you find a solution? Thanks!
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