Hello

See these links here 

Hope the help 

Good Luck

http://changlab.stanford.edu/atac-seq.pdf

http://biorxiv.org/content/biorxiv/early/2016/01/15/036798.full.pdf

https://ar.scribd.com/doc/260319675/Protocol-ATAC-Seq

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/

http://www.illumina.com/content/dam/illumina-marketing/documents/products/research_reviews/sequencing-methods-review.pdf

Thank you Saleh! Those are really helpful~

I don't know enough of your experiment and the results, but just an idea- as we see it sometimes on LabChip - the gel image result  resembles on what we see when we overload the sample. Here it seems controls are overloaded causing (if possible, never worked with tapestation)  clogging of the capillaries. Did you try to dilute control libraries and then load everything again, after you run some sort of rinsing protocol? 

do you have gel picture before Ampure step? sometimes Ampure is the problem. moreover the good library should be from 200-1500 bp not from 50.. double check you protocol please

You're using the wrong kit. You need to use the Nextera DNA kit, not the XT!

Hi Dr. Wei,

I am currently trying the same protocol using different cell types and having the same kind of results. I also tried to dilute my samples before running into Tapestation but it didn´t work. Did you find a solution? If yes, would you mind to discuss it into details through email? I appreciate your help ([email protected]).

Kind regards

Vitor.

Hi Lu Wei,

Did you find out if this ATAC library was suitable for sequencing? If not, did you find a solution?

Kind regards,

Amy

hey...you should try both the elution kit and ampure beads for experiment. In my opinion the beads work far better than kit. after that you can compare results as well.

Question looks a bit old, but I'll throw in my 2 cents worth.

Use beads to simultaneously size select and clean. the patent finally ended on the AmpureXP Beads, so many companies are now offering identical products for much cheaper! I've been using Kapa Pure Beads from KapaBiosystems, subsidiary of Roche. They work well and are much cheaper than AmpureXP.

For ATAC libraries I do a 2-step size selection, which gets rid of both HMW/gDNA and LMW primers, giving you nice clean libraries without losing anything, nor picking up any contamination from the Qiagen column matrix.

Be certain to use the correct kit and library concentration on the Tapestation, as overloading it will give you spurious results. Then, rather than looking solely at the gel-like image, look at the actual size vs florescence trace! This gives a much better picture of the size distribution of your library than the gel-like smears.

For really good ATAC libraries you should ideally see progressively larger rounded peaks on the trace, representing 1) open chromatin, 2) single-nucleosome, 3) di-nucleosome, 4) tri-nucleosome, etc... regions. Gels, or gel-like images typically just look like a smear, with the open, single-, di- , tri-, etc... regions running together in a smear and difficult to distinguish. This is why I recommend looking at the trace rather than the gel-like images.

Hope this helps, & Best of luck!

Hi Stefan,

Why say that? I thought XT kit is just for small genome and same purpose of Nextera DNA kit. Please explain.

Thanks.

Lu

Hi all,

I am no longer working with ATAC-seq for quite a long time. But recent updates from my previous lab member is, the problem is probably focusing on ampure library cleanup steps. Please double check suitable ways for libraries purification.

Lu