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Forum: 454 Pyrosequencing 01-08-2009, 02:58 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Nimblegen are hosting a webinar very soon. See...

Nimblegen are hosting a webinar very soon. See here. (https://www1.gotomeeting.com/register/690745951)
Forum: 454 Pyrosequencing 08-07-2008, 02:44 AM
Replies: 61
Views: 93,847
Posted By sci_guy
We are bound by their standard protocol I think....

We are bound by their standard protocol I think. The service specifies delivery of 21 ug of DNA and they do the library prep and QC. The concatamerisation/shear/ligate Illumina adaptor method...
Forum: 454 Pyrosequencing 08-07-2008, 02:26 AM
Replies: 61
Views: 93,847
Posted By sci_guy
Excellent! Thank you Siqusn. Those numbers are...

Excellent! Thank you Siqusn. Those numbers are informative for us. One last question, are you capturing a contiguous region (less Windowmasker repeatmasked regions)?
We are capturing a contiguous 5...
Forum: 454 Pyrosequencing 08-06-2008, 06:46 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Hodges et al. reported that following something...

Hodges et al. reported that following something approximating your method they could get good Illumina GA-1 reads but suffered from poor sequence capture, whereas 500-mers could be captured OK but...
Forum: 454 Pyrosequencing 08-06-2008, 01:49 AM
Replies: 61
Views: 93,847
Posted By sci_guy
Hi Siqusn, So you don't see a large decrease...

Hi Siqusn,

So you don't see a large decrease in the number of reads per flow cell lane like that reported by Hodges et al. (http://www.nature.com/ng/journal/v39/n12/abs/ng.2007.42.html)? I would...
Forum: 454 Pyrosequencing 02-28-2008, 09:06 PM
Replies: 61
Views: 93,847
Posted By sci_guy
If your favourite DNase works processively then I...

If your favourite DNase works processively then I imagine will you see a big old smear on the gel. If the enzyme is non-processive and just creates dsDNA breaks then DNA size will be more tightly...
Forum: 454 Pyrosequencing 02-28-2008, 08:27 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Ultrasonicators

Yes. As I've found out either you, or your Next-gen service provider, needs a pretty funky new sonicator. It seems nebulisation won't cut it (bad pun :D) for 100 - 200 bp libraries. See these pieces...
Forum: 454 Pyrosequencing 02-28-2008, 04:43 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Reseq: Many thanks for the info! Horigen: No...

Reseq: Many thanks for the info!

Horigen: No one got back to me. But I have heard anecdotally that Nimblegen is on track to offer 385,000 probe chip enrichment as a service around the end of...
Forum: 454 Pyrosequencing 01-29-2008, 02:23 PM
Replies: 61
Views: 93,847
Posted By sci_guy
The HD2 array physically takes up 3.84-fold sized...

The HD2 array physically takes up 3.84-fold sized area over the first-gen chip and has a feature shrink down to 2/3 size:
3.84 / 0.666 =~ 5.7x potential probes by area
By actual probes calculation:...
Forum: 454 Pyrosequencing 01-29-2008, 02:07 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Okou et al.

Yes, you are quite right. Good spotting. I had become confused by the header on supplementary figure 1. 1 in 10 enrichment makes more sense and is in the same ballpark as Albert et al. Perhaps the...
Forum: 454 Pyrosequencing 01-25-2008, 01:56 PM
Replies: 61
Views: 93,847
Posted By sci_guy
Custom CGH

pmcget - It's my belief that Nimblegen will offer custom HD2 CGH chips around March.
Forum: 454 Pyrosequencing 01-24-2008, 05:04 PM
Replies: 61
Views: 93,847
Posted By sci_guy
I've been in contact with Roche and I am lead to...

I've been in contact with Roche and I am lead to believe that a Nimblegen sequence capture service will be available around March, not long after human custom HD2 chips hit the market.

I have some...
Forum: 454 Pyrosequencing 01-24-2008, 04:44 PM
Replies: 61
Views: 93,847
Posted By sci_guy
My two cents...

I'm a postdoc employed to sequence a candidate region of interest via next-gen sequencing methods.

Here are my thoughts on Nimblegen capture as bullet points ripped from a presentation I gave to...
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