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Forum: 454 Pyrosequencing 10-26-2010, 12:54 PM
Replies: 61
Views: 52,788
Posted By sigusn
We don't have anything published on Mouse yet....

We don't have anything published on Mouse yet. But here are some papers:
This one tests Nimblegen capture
http://www.ncbi.nlm.nih.gov/pubmed/20562348
Using Nimblegen capture on Horses...
Forum: 454 Pyrosequencing 10-26-2010, 08:14 AM
Replies: 61
Views: 52,788
Posted By sigusn
Hi We have done Nimblegen sequence capture on...

Hi
We have done Nimblegen sequence capture on dogs, horses, cows, mouse, humans, etc. All works fine. Just using the standard protocol from Nimblegen+Illumina should work fine, or use your own...
Forum: Bioinformatics 06-04-2010, 07:27 AM
Replies: 50
Views: 15,202
Posted By sigusn
Hi You can upload your own genomes into the...

Hi
You can upload your own genomes into the IGV. Just upload the exact same fasta file as you aligned to using MAQ.
Forum: Bioinformatics 06-04-2010, 06:21 AM
Replies: 50
Views: 15,202
Posted By sigusn
Hi I gave up on using maqview. Use this free...

Hi
I gave up on using maqview. Use this free tool instead, The Integrative Genomics Viewer (IGV).
http://www.broadinstitute.org/igv/
Forum: Bioinformatics 01-15-2009, 03:45 PM
Replies: 50
Views: 15,202
Posted By sigusn
Hi I just downloaded the latest MAQ and...

Hi
I just downloaded the latest MAQ and MAQviewer, and when I try to view my alignments, MAQview shuts down after few mouse clicks and scrolling with the message: "Bus error". Is there a limitation...
Forum: Illumina/Solexa 10-03-2008, 04:48 AM
Replies: 145
Views: 286,539
Posted By sigusn
Can someone explain to me why the Illumina...

Can someone explain to me why the Illumina adapters need to be 5-phosphorylated? In the very similar SOLiD sample prep protocol the adapters are not phosphorylated.:confused:
Forum: Illumina/Solexa 10-01-2008, 02:43 AM
Replies: 8
Views: 2,674
Posted By sigusn
I've seen this too after using sequence capture...

I've seen this too after using sequence capture for sample prepp. and it would be interesting to get an explanation for this. I got this reply from Illuminas Tech support :
"My understanding is that...
Forum: 454 Pyrosequencing 08-31-2008, 12:08 PM
Replies: 61
Views: 52,788
Posted By sigusn
Some references> Okou et al. Nat Methods. 2007...

Some references>
Okou et al. Nat Methods. 2007 Nov;4(11):907-9
Excelent method description in the supplement

Hodges et al. Nat Genet. 2007 Dec;39(12):1522-7.
Describe the sequence capture...
Forum: 454 Pyrosequencing 08-26-2008, 01:22 AM
Replies: 61
Views: 52,788
Posted By sigusn
pooled DNA

Yes, I have tried pooling 4 samples and use the Nimblegen Seqcap arrays. With average sequence coverage of 40-50X I think I can say that works OK.
Forum: 454 Pyrosequencing 08-12-2008, 10:12 AM
Replies: 61
Views: 52,788
Posted By sigusn
Hi I hybridized for 65h. After elution I used...

Hi
I hybridized for 65h. After elution I used speedvac to dry down the sample, then dissolved in water. I did not get as much as Okou et al but enough to perform the PCR step and then the PCR...
Forum: Bioinformatics 08-11-2008, 11:52 PM
Replies: 9
Views: 3,739
Posted By sigusn
Im having exact the same problem with SOAP on my...

Im having exact the same problem with SOAP on my MacBook Pro. But the Novoalign software works OK.
Forum: 454 Pyrosequencing 08-11-2008, 11:49 PM
Replies: 61
Views: 52,788
Posted By sigusn
Elution step

Hi Lambroso
The elution step is well described in the Okou et al. paper. (Nature Methods 2007). However i did not have any equipment from Nimblegen for this. So I used home made system, cutout...
Forum: General 08-08-2008, 12:54 AM
Replies: 2
Views: 3,520
Posted By sigusn
Hi Matt You can order custom sequence capture...

Hi Matt
You can order custom sequence capture arrays from Nimblegen for any species and do the enrichment yourself, the service they provide is only for human/mouse. I have just tested it and it...
Forum: 454 Pyrosequencing 08-07-2008, 01:32 AM
Replies: 61
Views: 52,788
Posted By sigusn
Yes Im capturing 6 separate contiguous regions...

Yes Im capturing 6 separate contiguous regions total 1.25 Mb. If you are doing the seq-cap as a service at Nimblegen, will you have the option of using shorter fragments with Illumina adapters, or do...
Forum: 454 Pyrosequencing 08-07-2008, 01:02 AM
Replies: 61
Views: 52,788
Posted By sigusn
Hi Hodges et al write “For optimal sequence...

Hi
Hodges et al write “For optimal sequence generation on the Illumina platform, fragments of less than 250 bp in length are desirable. This was below the size range initially optimized for capture....
Forum: Introductions 08-06-2008, 01:36 AM
Replies: 0
Views: 4,788
Posted By sigusn
Smile Hej from Sweden

Hi
Im a post-doc at Uppsala University, Uppsala Sweden.
I'm working with sequence capture technologies and Illumina/Solexa sequencing and in the future also SOLiD.
Forum: 454 Pyrosequencing 08-06-2008, 12:54 AM
Replies: 61
Views: 52,788
Posted By sigusn
I sonicated the DNA to 100-300 bp, followd the...

I sonicated the DNA to 100-300 bp, followd the Illumina protocol for adding adapters, then seq-cap with Nimblegen arrays, PCR and Sequenced on Illumina GA-1. It worked out all right. I have not...
Forum: SOLiD 08-06-2008, 12:46 AM
Replies: 5
Views: 3,110
Posted By sigusn
I have sonicated the DNA down to 100-300 bp, and...

I have sonicated the DNA down to 100-300 bp, and then performed sequence capture with Nimblegen arrays and sequenced on the Solexa systems. Works fine, should work as well with the SOLiD system or ?
Forum: 454 Pyrosequencing 08-06-2008, 12:36 AM
Replies: 61
Views: 52,788
Posted By sigusn
Hi I have just tested the Nimblegen Sequence...

Hi
I have just tested the Nimblegen Sequence capture for Solexa sequencing and it works fine if you have good quality 20ug input DNA. WGA samples worked but with more variation in the sequence...
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