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Old 05-21-2018, 04:28 PM   #1
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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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File Type: jpg Library validation small file.jpg (58.2 KB, 184 views)
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Old 05-21-2018, 05:19 PM   #2
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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, 12:00 PM   #3
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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, 07:34 AM   #4
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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, 05:09 AM   #5
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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, 09:17 AM   #6
Location: Baton Rouge, Louisiana

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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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Last edited by RickC7; 06-14-2018 at 09:25 AM.
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Old 12-11-2018, 01:01 AM   #7
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Did you solve this? My libraries look like yours
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Old 03-01-2019, 06:55 AM   #8
Marķa Camila Fetiva
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Default Does my library look ok?

Hello, I performed ATACseq preparation of librarys I used 50.000 cells counted by en bauer chamber, and following the protocol of Buen rostro, I did 25 cycles in total of PCR. Can someone tell me if this library looks ok? (attached pdf 1st sample) I am not sure about it. Thank you so much for your help


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File Type: pdf 20190227_Fragment analizer.pdf (444.4 KB, 54 views)
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atac, hs d1000, library

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