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Forum: Sample Prep / Library Generation 06-21-2017, 07:26 AM
Replies: 2
Views: 1,109
Posted By NickPantelireis
I can't seem to figure out if when doing ATAC-seq...

I can't seem to figure out if when doing ATAC-seq you need to maintain the selected cycles the same throughout samples? For example I have 4 samples and I'm doing n=3. So do I select the number of...
Forum: Sample Prep / Library Generation 06-16-2017, 05:13 AM
Replies: 15
Views: 4,033
Posted By NickPantelireis
It's looking better :) Is there any reason you're...

It's looking better :) Is there any reason you're using NP-40 and not Digititonin or even Igepal during this step? I read that NP-40 is very powerful and lyses all membranes in the cell, while the...
Forum: Sample Prep / Library Generation 06-14-2017, 01:25 AM
Replies: 15
Views: 4,033
Posted By NickPantelireis
Hey, I'm by no means an expert in this but...

Hey,

I'm by no means an expert in this but assuming this trace is done at the end of your protocol it looks like the DNA is underdigested. From the published protocol it could be down to cell...
Forum: Sample Prep / Library Generation 03-15-2017, 03:29 AM
Replies: 20
Views: 12,688
Posted By NickPantelireis
Hi Jubs, How did you measure the mtDNA...

Hi Jubs,

How did you measure the mtDNA content with qPCR. Was it an absolute measurement or a relative comparison? I've been thinking of doing a qPCR for a housekeeping gDNA gene and a mtDNA gene...
Forum: Sample Prep / Library Generation 03-15-2017, 02:17 AM
Replies: 15
Views: 4,033
Posted By NickPantelireis
Ah yeah, I see what you mean. It does look like...

Ah yeah, I see what you mean. It does look like the DNA is underdigested or as you said not digested at all. With PCR you should be able to see if your primers attach to your DNA. If not then the...
Forum: Sample Prep / Library Generation 03-14-2017, 08:52 AM
Replies: 15
Views: 4,033
Posted By NickPantelireis
I read somewhere in one of the other posts on...

I read somewhere in one of the other posts on here that after the tagmentation you still need to amplify your DNA using PCR if you haven't already. The amount of DNA after tagmentation is quite a low...
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