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Forum: 454 Pyrosequencing 10-26-2010, 01:54 PM
Replies: 61
Views: 93,934
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, 09:14 AM
Replies: 61
Views: 93,934
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: 454 Pyrosequencing 08-31-2008, 01:08 PM
Replies: 61
Views: 93,934
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, 02:22 AM
Replies: 61
Views: 93,934
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, 11:12 AM
Replies: 61
Views: 93,934
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: 454 Pyrosequencing 08-12-2008, 12:49 AM
Replies: 61
Views: 93,934
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: 454 Pyrosequencing 08-07-2008, 02:32 AM
Replies: 61
Views: 93,934
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, 02:02 AM
Replies: 61
Views: 93,934
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: 454 Pyrosequencing 08-06-2008, 01:54 AM
Replies: 61
Views: 93,934
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: 454 Pyrosequencing 08-06-2008, 01:36 AM
Replies: 61
Views: 93,934
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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