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Forum: 454 Pyrosequencing 12-16-2010, 09:04 AM
Replies: 15
Views: 4,008
Posted By jOn
It is the oil

We've had 50% enrichment with the new SV oils even after halving the cpb. Switched back to a stock of old oils last week and the problem disappeared. There is definitely something different about the...
Forum: 454 Pyrosequencing 12-01-2010, 06:30 AM
Replies: 15
Views: 4,008
Posted By jOn
Guys I've been using plastic strip caps and the...

Guys I've been using plastic strip caps and the usual low bind plates from eppendorf (always have) and never once had a broken emulsion - my problems appear to be new oil related.
Forum: 454 Pyrosequencing 11-19-2010, 10:30 AM
Replies: 11
Views: 3,639
Posted By jOn
Hi MEJ - I'm pretty convinced it could be the...

Hi MEJ - I'm pretty convinced it could be the oil - at least in my case - drop me a message and we'll swap LOT numbers.

jOn
Forum: 454 Pyrosequencing 11-16-2010, 10:23 AM
Replies: 15
Views: 4,008
Posted By jOn
emPCR issues

Enrichment following SV emPCR has quite dramatically increased with the last few preps. We're well used to doing a range of library preps and subsequent emPCR for both amplicon and shotgun using the...
Forum: The Pipeline 11-02-2010, 02:53 AM
Replies: 5
Views: 3,849
Posted By jOn
Exciting indeed eco

I think the next 2 years is going to be great viewing for the impartial observer - and this site will probably give a pretty good front row seat!
Forum: The Pipeline 11-01-2010, 10:11 AM
Replies: 5
Views: 3,849
Posted By jOn
Roche, DNA Electronics Partner on Semiconductor-based Sequencing

http://www.genomeweb.com//node/953678?hq_e=el&hq_m=858000&hq_l=2&hq_v=7a0dc9a075
Forum: SOLiD 07-15-2009, 01:21 AM
Replies: 7
Views: 4,243
Posted By jOn
Many thanks - that member# of yours is pretty...

Many thanks - that member# of yours is pretty Rock n Roll too.
Forum: SOLiD 07-14-2009, 03:06 AM
Replies: 7
Views: 4,243
Posted By jOn
Hi westerman, I was just wondering if you'd had...

Hi westerman, I was just wondering if you'd had any experiences that you could feed back relating to this link. We currently have a 454 and are debating on what platform to invest in next. Any...
Forum: 454 Pyrosequencing 07-10-2009, 07:04 AM
Replies: 1
Views: 1,935
Posted By jOn
Different NextGen platforms sharing the same space

Our group has a 454 sequencer with the workflow split over two rooms Lab 1) Library prep and emPCR set-up Lab 2) emulsion breaking, enrichment and sequencing (sequencer is also in lab 2).

My...
Forum: Literature Watch 07-02-2009, 09:36 AM
Replies: 2
Views: 1,686
Posted By jOn
Genomics: catch me if you can

A nice summary of target specific sequencing methods

http://www.nature.com/nmeth/journal/v6/n7/pdf/nmeth0709-539.pdf
Forum: Bioinformatics 06-04-2009, 04:17 AM
Replies: 0
Views: 1,614
Posted By jOn
'Bioinformatics for Next Generation Sequencing' virtual issue.

Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread. Many tools and algorithms relevant to next-generation sequencing...
Forum: 454 Pyrosequencing 04-17-2009, 01:23 AM
Replies: 34
Views: 14,652
Posted By jOn
Hi Gerald Are you doing a size exclusion...

Hi Gerald

Are you doing a size exclusion with the cDNA and a titration (concentrate the titration at the lower end)? Also, because fragment size is usually shorter for cDNA it may be worth...
Forum: 454 Pyrosequencing 04-16-2009, 06:24 AM
Replies: 34
Views: 14,652
Posted By jOn
For the reasons already pointed out by kmcarr ...

For the reasons already pointed out by kmcarr

"Compared to genomic DNA sequencing cDNA sequencing generally produces fewer filter passed reads (more failures due to mixed reads) and the mean...
Forum: Bioinformatics 02-04-2009, 03:35 AM
Replies: 8
Views: 3,895
Posted By jOn
What NextGen LIMS do you use?

I know "cquincer" started a very similar post to this back at the start of December last year. There wasn't a great deal of feedback at the time and I was wondering if anyone could offer some up to...
Forum: The Pipeline 01-12-2009, 04:50 AM
Replies: 4
Views: 6,678
Posted By jOn
Oxford Nanopore and Illumina Announce Strategic Alliance

Very interesting news
http://www.nanoporetech.com/press_releases/detail/104
Forum: Site Announcements 11-20-2008, 04:10 AM
Replies: 9
Views: 4,888
Posted By jOn
Well done ECO, I can see this being of particular...

Well done ECO, I can see this being of particular benefit to people new to NextGen sequencing that probably donít own a machine but are interested in applying for grants etc; it will definitely...
Forum: 454 Pyrosequencing 11-08-2008, 06:10 AM
Replies: 3
Views: 4,270
Posted By jOn
I saw this poster being presented at a recent...

I saw this poster being presented at a recent GS-FLX userís group meeting in London. I got the impression that 454 Branford had primarily implemented this technology in order to scale up their sample...
Forum: 454 Pyrosequencing 10-24-2008, 08:06 AM
Replies: 0
Views: 2,396
Posted By jOn
Mixed fragment size normalized cDNA sequencing

I was just wondering what general approach and experience groups have had sequencing mixed fragment size cDNA (transcriptome sequencing LMW 70 – 500 bp AND > 1.5 kb in one sample). Not only that, but...
Forum: 454 Pyrosequencing 10-08-2008, 08:02 AM
Replies: 2
Views: 2,767
Posted By jOn
Sorry if this reply is a little on the late side...

Sorry if this reply is a little on the late side - only just joined the site! We've used kit's close to the sell by date before. Your biggest worry would be a sequencing kit, the sell by date on this...
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