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Old 05-21-2018, 03:28 PM   #1
coralxanpu
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Default Is my ATACseq library okay?

We are new to ATAC-Seq. We have performed library validation and several of our samples have produced results similar to those in the image attached. We have a single large peak at 186 bp. Are we okay to go ahead for sequencing? Thanks a lot.
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Old 05-21-2018, 04:19 PM   #2
coralxanpu
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I forgot to mention that above samples are from FACS mouse cells. We also tried IP instead of FACS, which gave us multiple small peaks, which method shall I go on? Any suggestion is greatly appreciated.
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Old 05-23-2018, 11:00 AM   #3
pmiguel
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We run qc chips for people doing ATACseq with some frequency. I'm never sure what a "good" result is.
I guess you want a large percentage of your DNA to be in the nucleosome monomer size range? But you also want to see some multimers? Not sure.
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Old 05-30-2018, 06:34 AM   #4
Affef
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It seems that your library is over tagmented. Maybe you should decrease the incubation time while performing the tagmentation.
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Old 06-07-2018, 04:09 AM   #5
Simone78
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I would also say that it is over-tagmented. Which Tn5 are you using, Nextera or home-made? Maybe there is too much Tn5 for the number of cells you are using?
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Old 06-14-2018, 08:17 AM   #6
RickC7
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Here is what my ATAC libraries look like. I agree that optimization of tagmentation enzyme amount or time should be considered.

What is you input amount? Are you starting with <50,000 cells? Smaller input amounts will require less enzyme and/or shorter incubation.
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