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Forum: Ion Torrent 10-22-2014, 07:12 PM
Replies: 17
Views: 7,868
Posted By nextgen
If youare still looking, PCRClean DX is the...

If youare still looking, PCRClean DX is the choice.
Forum: Sample Prep / Library Generation 10-18-2013, 06:05 AM
Replies: 48
Views: 39,351
Posted By nextgen
When you say more effective, you mean the range...

When you say more effective, you mean the range of the DNA size, distribution or recovery?
Forum: RNA Sequencing 06-24-2012, 10:20 AM
Replies: 3
Views: 1,853
Posted By nextgen
RNA fragmentation

Hi:

What is your result with either Mg2+ or Zn2+ based buffer? I prefer Mg2+ based buffer but can't find any protocol. thanks,
Forum: Sample Prep / Library Generation 04-13-2012, 09:51 AM
Replies: 13
Views: 9,350
Posted By nextgen
Sizeselector from Aline Bio

You may talk to Tufts University core facility. They have some good experience. It is very effective in removing adaptor contamination.
Forum: Illumina/Solexa 09-02-2010, 12:06 PM
Replies: 32
Views: 16,790
Posted By nextgen
It is true that all the robots do is pipetting....

It is true that all the robots do is pipetting. However, if someone has spent the time writing up scripts and user interface and tuning up the process, it will really save a lot time and effort to...
Forum: Illumina/Solexa 09-01-2010, 05:36 PM
Replies: 32
Views: 16,790
Posted By nextgen
I wonder who is working on automated library...

I wonder who is working on automated library construction that is an open system so that you don't have to be tied up to a particular vendor. Some institutes have their own high throughput library...
Forum: Sample Prep / Library Generation 05-04-2010, 07:55 PM
Replies: 3
Views: 1,316
Posted By nextgen
Can you try betaine, DMSO to lower Tm?

Can you try betaine, DMSO to lower Tm?
Forum: Sample Prep / Library Generation 05-03-2010, 10:34 AM
Replies: 5
Views: 7,796
Posted By nextgen
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Forum: Sample Prep / Library Generation 05-03-2010, 10:32 AM
Replies: 5
Views: 7,796
Posted By nextgen
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Forum: Sample Prep / Library Generation 05-03-2010, 09:28 AM
Replies: 3
Views: 1,786
Posted By nextgen
Can you design a new PCR primer to include part...

Can you design a new PCR primer to include part of old adaptor sequence and the new adaptor sequence? When you re-amplify your library for a few cycles, the new adaptor sequence will be added.
Forum: 454 Pyrosequencing 05-02-2010, 08:57 PM
Replies: 2
Views: 4,376
Posted By nextgen
NEB, Enzymatics, Epicentre

NEB, Enzymatics, Epicentre
Forum: Illumina/Solexa 03-31-2010, 07:13 PM
Replies: 32
Views: 16,790
Posted By nextgen
Cost is an issue. Once you have bought the...

Cost is an issue. Once you have bought the system, you are lock into the system. You have to keep buying whatever they offer. Another issue is that we all know the the genomics field is evolving...
Forum: Sample Prep / Library Generation 03-26-2010, 08:14 PM
Replies: 5
Views: 7,796
Posted By nextgen
How much DNA do you recover after two rounds of...

How much DNA do you recover after two rounds of size selection?
Forum: Illumina/Solexa 03-24-2010, 06:58 AM
Replies: 32
Views: 16,790
Posted By nextgen
It is interesting that I heard of totally...

It is interesting that I heard of totally different stories.
Forum: Illumina/Solexa 03-17-2010, 07:58 PM
Replies: 32
Views: 16,790
Posted By nextgen
Use Sizeselector and you will not need double...

Use Sizeselector and you will not need double selection. Too much loss of DNA with double selection.
Forum: Illumina/Solexa 03-17-2010, 07:06 PM
Replies: 32
Views: 16,790
Posted By nextgen
This machine has a few characteritics based on...

This machine has a few characteritics based on anecdotes I heard so far:
1, you get 10% yield, which means 3 to 4 more cycles of PCR to compensate for the loss. Lib bias may be generated from PCR....
Forum: Sample Prep / Library Generation 02-16-2010, 03:48 PM
Replies: 13
Views: 9,350
Posted By nextgen
Check this out: ...

Check this out:
http://www.genomeweb.com/sage-science-automates-dna-fractionation-next-gen-sequencing.

Double selection means you do the same selection twice. You will lose more DNA with each...
Forum: Sample Prep / Library Generation 02-15-2010, 12:36 PM
Replies: 10
Views: 3,180
Posted By nextgen
Size selection method was published first about...

Size selection method was published first about adjusting PEG and salt concentration to cause the selective binding of DNA molecules with certain size. The Ampure method used beads to replace...
Forum: Illumina/Solexa 02-15-2010, 10:02 AM
Replies: 9
Views: 3,362
Posted By nextgen
Co-ask. I am interested in who is doing it and...

Co-ask. I am interested in who is doing it and what advantage can be offered.
Forum: Sample Prep / Library Generation 02-14-2010, 07:33 AM
Replies: 27
Views: 7,201
Posted By nextgen
Some of the DNA is damaged during shearing. My...

Some of the DNA is damaged during shearing. My experience has been under certain conditions, only half of the ends can be repaired on one molecule. I don't know the reason yet, but I think the DNA...
Forum: Sample Prep / Library Generation 02-14-2010, 07:13 AM
Replies: 15
Views: 5,734
Posted By nextgen
I used 500bp range as this right range for 454...

I used 500bp range as this right range for 454 (some mRNA transcripts are in that range.) You can easily get smaller size. But for random or end-to-end cDNa synthesis, 500bp is better.
Forum: Sample Prep / Library Generation 02-14-2010, 07:10 AM
Replies: 15
Views: 5,734
Posted By nextgen
Covaris works great for RNA shearing. You can get...

Covaris works great for RNA shearing. You can get a very tight range. Just play around with it.
Forum: Sample Prep / Library Generation 02-14-2010, 06:58 AM
Replies: 13
Views: 9,350
Posted By nextgen
The reason is that you have a lot DNA at 130....

The reason is that you have a lot DNA at 130. Ampure size selection is not as tight. When you have a lot DNA in the vicinity of your target size, it will just carry over. A double selection or...
Forum: Sample Prep / Library Generation 02-14-2010, 06:29 AM
Replies: 48
Views: 39,351
Posted By nextgen
Ampure

Ampure is just more expensive. Some of the time saved is just from reducing drying time. I think PCRClean is better in terms of band tightness.
Forum: Sample Prep / Library Generation 02-14-2010, 06:25 AM
Replies: 10
Views: 3,180
Posted By nextgen
Auto Library

Ampure is suitable for small size DNA selection especially when recovery is a concern, which is within the range Illumina. For large size DNA selection, Aline bioscience's PCRclean actually works...
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