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  • 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.
    Attached Files

  • #2
    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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    • #3
      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.
      --
      Phillip

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      • #4
        It seems that your library is over tagmented. Maybe you should decrease the incubation time while performing the tagmentation.

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        • #5
          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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          • #6
            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.
            Attached Files
            Last edited by RickC7; 06-14-2018, 08:25 AM.

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            • #7
              same profile

              Did you solve this? My libraries look like yours

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              • #8
                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

                Best

                Camila
                Attached Files

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