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Old 06-26-2017, 03:01 PM   #1
nclrsqr
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Location: San Francisco, CA

Join Date: Jul 2016
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Default ATACseq total amplification cycle number

I am optimizing my ATACseq and have questions about the normal range of total PCR cycle number.

What is the total number of PCR cycles people get for their ATACseq runs? Mine has been usually the initial 5 cycles + 8-15 additional cycles (depending on the run). The high total amp cycle feels shaky since the original ATACseq paper cited 10-12 total cycles (i.e. 5 initial cycle + 5-7 additional ones). I recently did a 25K to 100K cell curve, but PCR cycle # was not proportional to cell number. I followed the protocol exact, but this has been a persisting issue since the beginning.

Do people have any insight or experience with this? Thank you so much!
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Old 02-21-2018, 11:00 AM   #2
bman
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Default

Hey, I have a similar issue. Mine have been hitting the 1/3 max fluorescence threshold at around 8-10 additional cycles but I have been hesitant to do many more above the recommended. Did you ever figure this out/has it been an issue after sequencing?
Thanks!
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