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Forum: Bioinformatics 01-25-2017, 02:04 AM
Replies: 3
Views: 3,870
Posted By nanos
Dear Eric, we are very often analyzing sRNA data...

Dear Eric, we are very often analyzing sRNA data and I can give you some insight.
1) Adaptor trimming is really a must. With the minimum sequencing length being 50 you always have adaptor remnants...
Forum: Oxford Nanopore 01-16-2017, 12:38 AM
Replies: 32
Views: 23,162
Posted By nanos
Your friends are Trizma powder, water, HCl and a...

Your friends are Trizma powder, water, HCl and a well calibrated ph-meter ;-)
Forum: Oxford Nanopore 01-10-2017, 12:55 PM
Replies: 3
Views: 3,666
Posted By nanos
The MAP*** kits are outdated versions and are no...

The MAP*** kits are outdated versions and are no longer available.
The selection of kit depends on your sample type:
RAD - rapid kit tagmenting the template DNA
Lig1D - Ligation of adaptors...
Forum: Oxford Nanopore 09-12-2016, 02:02 PM
Replies: 32
Views: 23,162
Posted By nanos
The Tris-HCl is used for the elution from Ampure...

The Tris-HCl is used for the elution from Ampure beads. As far as I know the higher pH facilitates the resolubilization of high molecular weight DNA.
You can definitely use pH8, but you might loose...
Forum: Oxford Nanopore 07-27-2016, 12:58 AM
Replies: 32
Views: 23,162
Posted By nanos
@Markiyan, if I may ask, how do you degas these...

@Markiyan, if I may ask, how do you degas these buffers?
Forum: Oxford Nanopore 07-21-2016, 11:27 PM
Replies: 32
Views: 23,162
Posted By nanos
maybe also add the NEBNext FFPE DNA Repair mix to...

maybe also add the NEBNext FFPE DNA Repair mix to repair the input DNA for the standard protocol. This was shown to increase sequence quality and length quite a bit.
Forum: Sample Prep / Library Generation 07-18-2015, 07:47 AM
Replies: 6
Views: 4,328
Posted By nanos
If you want to go for Y-shaped adaptors, you can...

If you want to go for Y-shaped adaptors, you can also just order the two strands as oligo (best is HPLC purified) and perform a simple annealing reaction before you do the ligation. We did that for a...
Forum: Sample Prep / Library Generation 07-12-2015, 03:44 AM
Replies: 6
Views: 4,328
Posted By nanos
Hi, we always use the NEB adaptor and in our...

Hi,

we always use the NEB adaptor and in our hands it is clearly superior in terms of ligation efficiency compared to the Standard Y-shaped adaptors.

I don't know the current version of the...
Forum: RNA Sequencing 02-02-2011, 04:44 AM
Replies: 39
Views: 16,270
Posted By nanos
Hi, I recently did my first ScriptSeq mRNA...

Hi,

I recently did my first ScriptSeq mRNA libraries.

I am now analyzing the data and I see huge amounts of antisense reads mapping to the genes. I already did strand specific mRNAseq with a...
Forum: Vendor Forum 07-08-2010, 12:43 AM
Replies: 45
Views: 21,203
Posted By nanos
Is it possible to use this kit for Drosophila...

Is it possible to use this kit for Drosophila melanogaster mRNA purification?
Forum: Illumina/Solexa 05-31-2010, 11:11 PM
Replies: 145
Views: 321,119
Posted By nanos
hi!! i would like to use custom adaptors to...

hi!!

i would like to use custom adaptors to do ChiP sequencing.

for this i would need to know what the concentration of the adaptor for this protocol is.

thanks for your help
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