Hi everyone! I'm performing ATAC-seq to determine open chromatin regions of a cell line. I went through the protocol and wonder if there are means to verify during the whole procedure if we are getting a result or even a glimpse of the result? Like a stop-point and see a preview of the end-product. Is there such a way? or the closest thing is performing library-quality through bioanalyzer after PCR amplification? Thank you very much in advance.
Oh, there is actually a stopping point before PCR amplification, wherein we can store the purified DNA at -20 after tagmentation and before PCR amplification. Is there a way or possibility that at this stop point, we can have a preview of the result or check whether we are doing the right thing? Thanks once again. Keep safe!
It's clear now. I'm just curious that is why I asked the question. Thank you very much, ATpoint, for the response. Keep safe!
Sure thing. I know by experience that it is tempting to know early on whether the experiment worked fine, unfortunately with NGS this is not possible most of the time. A shallow sequencing is sometimes a good idea, e.g. for ChIP-seq where success is not guaranteed and strongly dependent on factors such as antibody and sonication/IP conditions. ATAC-seq (in my hands for human and mouse) kind of always works. In the end only the sequencing itself tells you success/failure.
Yeah, it is really tempting. I guess I just have to really wait for the sequencing then. Big thanks again.
Oh! I have other questions but not related to the previous one.
P.S. I actually saw your response to one of the questions asked on the link: ATAC-seq 150bp reads .
Thank you!
Do what is cheapest. If you have agood quote for a Novaseq run where 2x150 is often standard then do this, or if 2x50 is cheaper then go for this one. We usually do 2x50bp.
Big, big thanks ATpoint. Keep safe.