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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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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. -
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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PhillipComment
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It seems that your library is over tagmented. Maybe you should decrease the incubation time while performing the tagmentation.Comment
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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?Comment
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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.Last edited by RickC7; 06-14-2018, 08:25 AM.Comment
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same profile
Did you solve this? My libraries look like yoursComment
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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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CamilaComment
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Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
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