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Forum: Illumina/Solexa 01-19-2017, 11:05 AM
Replies: 27
Views: 5,496
Posted By Yepler
I went through IDT. There's a little bit of lead...

I went through IDT. There's a little bit of lead time, since the LNA bases go through Exiqon - if you have a direct account with Exiqon already, that may save you some time.
Forum: Sample Prep / Library Generation 01-11-2017, 07:46 AM
Replies: 6
Views: 3,661
Posted By Yepler
MagQuant/Omega beads worked well in my hands if...

MagQuant/Omega beads worked well in my hands if there was plenty of PCR product going into the cleanup.

MagBio beads I never even tested; a chat with a customer service rep there helped me...
Forum: Illumina/Solexa 01-11-2017, 07:39 AM
Replies: 10
Views: 3,206
Posted By Yepler
To the best of my ability to tell, I think those...

To the best of my ability to tell, I think those should work out for you. Good luck, and please do let me know how it turns out.
Forum: Illumina/Solexa 01-06-2017, 01:08 PM
Replies: 10
Views: 3,206
Posted By Yepler
I used the Read 1 Sequencing Primer from Illumina...

I used the Read 1 Sequencing Primer from Illumina as a baseline for the Tm calculations ('cause yes, all calculators seem different!).

There are now three LNA bases in my primer, in the middle of...
Forum: Illumina/Solexa 01-05-2017, 10:12 AM
Replies: 27
Views: 5,496
Posted By Yepler
http://seqanswers.com/forums/showthread.php?t=7125...

http://seqanswers.com/forums/showthread.php?t=71254 has some details.

I'm not familiar with SuperSAGE, but I took a quick look at the M&M from a paper, and I think we may have the same issue. ...
Forum: Illumina/Solexa 01-04-2017, 08:20 AM
Replies: 27
Views: 5,496
Posted By Yepler
Yep. I had the exact same issue (two lanes okay,...

Yep. I had the exact same issue (two lanes okay, two lanes pretty much all poly-G) when using a custom sequencing primer on the NextSeq. The NS is really sensitive to primer Tm. Are you using a...
Forum: Illumina/Solexa 12-12-2016, 02:33 PM
Replies: 3
Views: 1,506
Posted By Yepler
Yep, you can do asymmetrical runs on the NextSeq....

Yep, you can do asymmetrical runs on the NextSeq. I don't know about the length question (sorry - my run was 50/26). I *have* seen that as the sequencing proceeds, the quality goes down, so I'd be...
Forum: Sample Prep / Library Generation 10-28-2016, 11:48 AM
Replies: 6
Views: 3,661
Posted By Yepler
My group has used ALine kits with good success; I...

My group has used ALine kits with good success; I recommend either their v2 or v3 kits. The only caveat is that if you have very low concentration libraries, then you may have more variability or it...
Forum: Illumina/Solexa 09-27-2016, 11:44 AM
Replies: 10
Views: 3,206
Posted By Yepler
Sorry it took me a few days to check back. I...

Sorry it took me a few days to check back. I might have identified your problem, although it might also be colored by my own experiences.

I have quite small-insert libraries, and while they are...
Forum: Illumina/Solexa 09-22-2016, 06:12 PM
Replies: 10
Views: 3,206
Posted By Yepler
If you're still having the issue, send me a...

If you're still having the issue, send me a message; I had to do some dancing to get custom primers to work on the NextSeq and might be able to help out.
Forum: Core Facilities 02-18-2016, 12:15 PM
Replies: 5
Views: 2,877
Posted By Yepler
Sort of delayed response, but...

Hey, I have two! And I've seen a couple others in the field. Do you have questions about the Dx?

I'd be interested in hearing from other Dx owners about their experience with running these...
Forum: Illumina/Solexa 01-22-2015, 03:02 PM
Replies: 24
Views: 6,762
Posted By Yepler
Hmmm, one other thing to check is whether the...

Hmmm, one other thing to check is whether the flow cell is all snapped together. I had the same issue (unable to focus - probably because there was nothing to focus on), and the flow cell housing...
Forum: Illumina/Solexa 09-06-2013, 12:08 PM
Replies: 8
Views: 3,962
Posted By Yepler
Awesome, that was exactly what I wanted to know....

Awesome, that was exactly what I wanted to know. Thank you for such speedy replies.

@microgirl123: Fortunately, a loud fan will be okay, I'm getting our old "tissue culture room" - which, to my...
Forum: Illumina/Solexa 09-06-2013, 07:50 AM
Replies: 8
Views: 3,962
Posted By Yepler
How about the learning curve?

Hi, all-

Happy Friday! I'm here looking for some advice from MiSeq owners.

I just received grant funding and am planning to purchase a MiSeq as part of the project plan. Previous to this,...
Forum: Illumina/Solexa 10-25-2012, 12:31 PM
Replies: 2
Views: 4,249
Posted By Yepler
Take a look at the supplemental info here: ...

Take a look at the supplemental info here:

David Bentley in Nature (2008) 456, 53-59 Accurate whole human genome sequencing using reversible terminator chemistry (supplementary material:...
Forum: Illumina/Solexa 07-03-2012, 08:01 AM
Replies: 37
Views: 36,841
Posted By Yepler
Take a look at the supplemental info here: ...

Take a look at the supplemental info here:

David Bentley in Nature (2008) 456, 53-59 Accurate whole human genome sequencing using reversible terminator chemistry (supplementary material:...
Forum: Illumina/Solexa 06-26-2012, 12:21 PM
Replies: 37
Views: 36,841
Posted By Yepler
Just wanted to update (in case this helps someone...

Just wanted to update (in case this helps someone else) and say that changing to the longer P5 sequence solved the problem. MiSeq returned an avalanche of good reads!
Forum: Illumina/Solexa 06-13-2012, 03:01 PM
Replies: 37
Views: 36,841
Posted By Yepler
Thanks, skosuri, for posting your solution. I...

Thanks, skosuri, for posting your solution. I have been having the same problem...(homebrew) library looked fine on previous HiSeq runs, but wouldn't form clusters on a MiSeq. Looks like I have the...
Forum: Illumina/Solexa 05-23-2011, 12:37 PM
Replies: 5
Views: 3,336
Posted By Yepler
Thanks for the responses...I contacted someone...

Thanks for the responses...I contacted someone from Illumina who agreed that it should be fine (although she was nervous about degradation).
Forum: Illumina/Solexa 05-18-2011, 12:57 PM
Replies: 5
Views: 3,336
Posted By Yepler
Yep, we do! But it's normally denatured dsDNA...

Yep, we do! But it's normally denatured dsDNA and has both strands present. I want to know if I can load only one of those two strands and still get productive clusters - for simplicity's sake,...
Forum: Illumina/Solexa 05-18-2011, 10:16 AM
Replies: 5
Views: 3,336
Posted By Yepler
Loading a flow cell with ssDNA (one strand only)

Hi, all-

I'm wondering if anyone has experience with loading just one strand of a ds duplex onto a flow cell. In this case, it would be the antisense (3'--5') strand, so that elongation would...
Forum: Introductions 12-28-2010, 07:52 AM
Replies: 373
Views: 92,569
Posted By Yepler
Hi all- I'm a R&D scientist at a small...

Hi all-

I'm a R&D scientist at a small company in Arizona - we're interested in using small RNA sequencing techniques and I've been lurking in the forums for a few months now. This is a...
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