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Forum: Sample Prep / Library Generation 03-15-2016, 08:10 AM
Replies: 7
Views: 1,963
Posted By NextGenSeq
We found that with 1 ng of total RNA we routinely...

We found that with 1 ng of total RNA we routinely see adapter artifacts.
Forum: Illumina/Solexa 03-14-2016, 05:48 AM
Replies: 5
Views: 2,233
Posted By NextGenSeq
If he's trying to detect extremely low amounts of...

If he's trying to detect extremely low amounts of a mutant it may make sense.

I think the only way to do this is to amplify the region of interest with several sets of primers which give varying...
Forum: Oxford Nanopore 03-09-2016, 10:53 AM
Replies: 4
Views: 2,224
Posted By NextGenSeq
A Hammer Thrown at Big Brother?

Oxford Nanopore Technologies, the company that pioneered a new DNA analysis technique called nanopore sequencing, has remained secretive about the microscopic channel at the heart of its products....
Forum: The Pipeline 03-02-2016, 09:44 AM
Replies: 14
Views: 5,241
Posted By NextGenSeq
http://www.sciencemag.org/news/2016/03/gene-sequen...

http://www.sciencemag.org/news/2016/03/gene-sequencing-technology-sparks-patent-fight-shrouded-mystery
Forum: The Pipeline 03-02-2016, 09:39 AM
Replies: 14
Views: 5,241
Posted By NextGenSeq
But this company is using SBS chemistry which is...

But this company is using SBS chemistry which is basically a modification of Sanger sequencing which is about 40 years old.
Forum: The Pipeline 02-29-2016, 09:32 AM
Replies: 14
Views: 5,241
Posted By NextGenSeq
Copying 10 year old technology doesn't seem very...

Copying 10 year old technology doesn't seem very new to me.
Forum: Vendor Forum 02-25-2016, 04:44 AM
Replies: 7
Views: 1,754
Posted By NextGenSeq
Sorry, this is spam.

Sorry, this is spam.
Forum: General 02-25-2016, 04:39 AM
Replies: 7
Views: 1,479
Posted By NextGenSeq
Looks like ONT has become a threat. Illumina...

Looks like ONT has become a threat.
Illumina used to scoff at them.

Competition is good for customers. Illumina is a one-trick pony and their technology is headed to the glue factory.
Forum: Core Facilities 02-19-2016, 05:54 AM
Replies: 5
Views: 2,994
Posted By NextGenSeq
I'm surprised it's so low. They make $120...

I'm surprised it's so low. They make $120 million each quarter from less than 10,000 customers? No wonder their products are so expensive.
Forum: Illumina/Solexa 02-18-2016, 04:35 AM
Replies: 50
Views: 9,587
Posted By NextGenSeq
Illumina has extortionate prices? Shocking!

Illumina has extortionate prices?

Shocking!
Forum: Illumina/Solexa 01-28-2016, 08:15 AM
Replies: 33
Views: 5,072
Posted By NextGenSeq
Illumina will almost always send replacement...

Illumina will almost always send replacement reagents if you use a small amount of spike-in PhiX sequenced with your library AND the PhiX did not give good sequencing results. If the PhiX gives good...
Forum: Sample Prep / Library Generation 12-01-2015, 05:15 AM
Replies: 7
Views: 1,609
Posted By NextGenSeq
How much rRNA? We typically see about 25% if the...

How much rRNA? We typically see about 25% if the RNA is not degraded.
Forum: Sample Prep / Library Generation 12-01-2015, 05:09 AM
Replies: 5
Views: 1,472
Posted By NextGenSeq
We use the NuGen RNA-Seq V2. If your RNA is...

We use the NuGen RNA-Seq V2. If your RNA is degraded use the FFPE RNA-Seq V2.

It works with anything.
Forum: Sample Prep / Library Generation 11-20-2015, 07:53 AM
Replies: 8
Views: 2,605
Posted By NextGenSeq
Looks like real degradation to me.

Looks like real degradation to me.
Forum: Literature Watch 11-16-2015, 06:47 AM
Replies: 2
Views: 2,537
Posted By NextGenSeq
Yes, indels are a problem since 5 bp are read at...

Yes, indels are a problem since 5 bp are read at a time. If a homopolymer is longer than this it can't be resolved (currently). ONT admits this and is working on solutions to it.
Forum: Sample Prep / Library Generation 10-16-2015, 06:59 AM
Replies: 2
Views: 759
Posted By NextGenSeq
Every WGA method isn't that good.

Every WGA method isn't that good.
Forum: Sample Prep / Library Generation 09-28-2015, 09:20 AM
Replies: 3
Views: 1,002
Posted By NextGenSeq
No you use the same settings as for genomic DNA. ...

No you use the same settings as for genomic DNA. We do this all the time.
Forum: Illumina/Solexa 09-21-2015, 09:58 AM
Replies: 4
Views: 1,064
Posted By NextGenSeq
I forgot to mention that Illumina farmed out the...

I forgot to mention that Illumina farmed out the PM for our MiSeq to another company this year. They are probably doing this in other areas now too.
Forum: Illumina/Solexa 09-15-2015, 09:12 AM
Replies: 4
Views: 1,064
Posted By NextGenSeq
We get the PM but our MiSeq is old.

We get the PM but our MiSeq is old.
Forum: General 09-15-2015, 07:44 AM
Replies: 7
Views: 1,271
Posted By NextGenSeq
I think a PCR work station is a good idea. We...

I think a PCR work station is a good idea. We have a separate clean room where we work only with unamplified DNA or RNA. I would get a work station with a UV light. It doesn't have to have...
Forum: Illumina/Solexa 09-01-2015, 11:01 AM
Replies: 16
Views: 9,733
Posted By NextGenSeq
We find the miRvana kit from Lifetech works...

We find the miRvana kit from Lifetech works better than the Qiagen miRNAEasy kit for miRNA isolation.

The Bioo Small RNA V2 kit uses degenerate adapters which help to eliminate the severe ligation...
Forum: Ion Torrent 07-23-2015, 08:58 AM
Replies: 2
Views: 955
Posted By NextGenSeq
We had a problem with an NEBNext Ion Torrent...

We had a problem with an NEBNext Ion Torrent library but the Hi-Q worked fine with a library made using Ion Torrent reagents.

What library concentration are you using? We use 85 pM.
Forum: Illumina/Solexa 07-21-2015, 08:04 AM
Replies: 6
Views: 1,974
Posted By NextGenSeq
Anything over 500 bp is not recommended.

Anything over 500 bp is not recommended.
Forum: Bioinformatics 06-23-2015, 05:27 AM
Replies: 6
Views: 1,833
Posted By NextGenSeq
If you barcode check the reads which are not...

If you barcode check the reads which are not de-multiplexed. Any reads which have a barcode you didn't make the libraries with are contamination.
Forum: Bioinformatics 06-12-2015, 07:02 AM
Replies: 11
Views: 5,637
Posted By NextGenSeq
It looks like Nextera bias to me.

It looks like Nextera bias to me.
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