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Forum: Pacific Biosciences 02-25-2013, 07:55 AM
Replies: 14
Views: 7,500
Posted By bkingham
The best have all been 1x120' movie, hot start...

The best have all been 1x120' movie, hot start with XL enzyme/C2 chemistry/C2 SMRT cell, 16kb library. We haven't tried XL/XL yet... soon.
It is starting to generate some impressive data
Forum: Pacific Biosciences 02-21-2013, 06:53 PM
Replies: 14
Views: 7,500
Posted By bkingham
PacBio read lengths.. How long?

Lately we've been running a number of 16-20kb libraries using XL enzyme and C2 chemistry. We're getting 30-35kb reads, and 25kb subreads... Only a few per run, but they definitely improve assembly....
Forum: Pacific Biosciences 02-21-2013, 06:41 PM
Replies: 12
Views: 5,358
Posted By bkingham
The # of productive ZMWs is influenced by the...

The # of productive ZMWs is influenced by the size of the library. We regularly get 50-55% with 2-6kb libraries, for 16kb libraries we can't get above 33%.... Lower than I'd like, but the reads are...
Forum: Illumina/Solexa 07-13-2011, 07:21 AM
Replies: 5
Views: 6,001
Posted By bkingham
I haven't done it... but did ask the question. It...

I haven't done it... but did ask the question. It can be done with no problem.
The v3 cluster kit advancement is more reads (bigger flow cell/more clustering real estate), and improved GC...
Forum: Sample Prep / Library Generation 08-09-2010, 07:56 AM
Replies: 0
Views: 2,601
Posted By bkingham
Mate-pair library prep for Illumina

Is there a group I can contract to make a single Illumina mate-pair library?
I only need 1, and don't want to buy a $$$ 10-prep kit
Forum: Sample Prep / Library Generation 08-09-2010, 07:50 AM
Replies: 13
Views: 7,851
Posted By bkingham
Covaris.... I've also used Hydroshear, Bioruptor....

Covaris.... I've also used Hydroshear, Bioruptor. The Covaris has been the most reproducible
Forum: De novo discovery 11-16-2009, 12:40 PM
Replies: 1
Views: 4,743
Posted By bkingham
de novo assembly and Illumina read length

We are preparing to do paired-end de novo sequencing on our GAIIx with the new kits. Is there a reason to run less than the maximum 100+ cycles on each end? There was a suggestion that the higher...
Forum: Illumina/Solexa 04-29-2009, 06:27 PM
Replies: 4
Views: 2,386
Posted By bkingham
I don't think I have ever ordered items w/...

I don't think I have ever ordered items w/ delivery in less than 2 weeks, then delayed further. I have found that by kindly 'badgering' my sales rep and FAS I can get partial delivery to keep me going
Forum: Illumina/Solexa 05-23-2008, 05:00 AM
Replies: 4
Views: 3,791
Posted By bkingham
Interesting.....I looked at the website that...

Interesting.....I looked at the website that shows the primer sequences, they appear to be different for all the kits - but I have used the same primer for PhiX, smRNA, and genomic sequencing. I...
Forum: Illumina/Solexa 05-22-2008, 03:51 PM
Replies: 4
Views: 3,791
Posted By bkingham
Yes, it is the same primer - also the same primer...

Yes, it is the same primer - also the same primer used for smRNA sequencing, would be helpful if they let us know if it were the same for all kits
Forum: General 05-22-2008, 03:48 PM
Replies: 3
Views: 3,938
Posted By bkingham
Before jumping in you should definitely get a...

Before jumping in you should definitely get a sense of what the PIs would get the most out of. While they are both considered next gen systems, short read and long read sequences are often very...
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