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Forum: Academic/Non-Profit Jobs 01-13-2016, 02:41 AM
Replies: 0
Views: 538
Posted By protist
Bioinformatician/Computational Biologist Position at the APC Microbiome Institute

Post-Doctoral Researcher or Senior Post-Doctoral Researcher – Computational Biologist/Bioinformatician – Gut Inflammation Research APC 3/ Spoke 7...
Forum: Illumina/Solexa 06-16-2013, 12:21 PM
Replies: 75
Views: 28,299
Posted By protist
I echo GW_OK & DNA_DAN with regard to the...

I echo GW_OK & DNA_DAN with regard to the nanodrop - should not be relied on for any library quantification at any stage. My advice if you want to quantify outside of your KAPA protocol use a QUBIT...
Forum: Sample Prep / Library Generation 03-06-2013, 12:14 AM
Replies: 10
Views: 2,998
Posted By protist
We have had our BioRupter for almost 5yrs and...

We have had our BioRupter for almost 5yrs and have had no issues with it. We are very careful to ensure that the unit is thoroughly cleaned and dried after each use and carry out regular tests with...
Forum: Illumina/Solexa 02-18-2013, 02:06 PM
Replies: 145
Views: 297,640
Posted By protist
The original adapters (what I called legacy)...

The original adapters (what I called legacy) released by Illumina are not exactly the same sequence as the currently in use TruSeq adapters - e.g. old adapters did not have indexes TruSeq ones do....
Forum: Illumina/Solexa 02-18-2013, 03:04 AM
Replies: 145
Views: 297,640
Posted By protist
The library schematic you are looking at is for...

The library schematic you are looking at is for legacy Illumina adapters not the the TruSeq versions. The original adapters required a PCR step to add the portion of the library that attaches to the...
Forum: The Pipeline 11-06-2012, 08:23 AM
Replies: 103
Views: 135,138
Posted By protist
Two interesting nuggets.. Oxford Nanopore to...

Two interesting nuggets..

Oxford Nanopore to Unveil New DNA Sequencers This Week
http://www.businessweek.com/news/2012-11-06/oxford-nanopore-to-unveil-new-dna-sequencers-this-week

Oxford...
Forum: Sample Prep / Library Generation 10-24-2012, 09:42 AM
Replies: 12
Views: 9,490
Posted By protist
Might be of help.....

Might be of help.....
Forum: Sample Prep / Library Generation 10-24-2012, 07:24 AM
Replies: 12
Views: 9,490
Posted By protist
You don't say how much DNA you actually have or...

You don't say how much DNA you actually have or the total volume only the ng/uL There a several kits out there for low starting amounts eg Nextera which is recommended for MiSeq..

Nextera XT kits...
Forum: Sample Prep / Library Generation 10-24-2012, 07:01 AM
Replies: 12
Views: 9,490
Posted By protist
Completely agree with pbluescript and in fact I...

Completely agree with pbluescript and in fact I personally would change that limit to 15-20 ng/uL. Nanodrop is good for 260/280 and 260/230 ratios but for accurate quantification at the lower 10 ng...
Forum: Events / Conferences 10-24-2012, 06:23 AM
Replies: 2
Views: 888
Posted By protist
The Broad Institute has a really nice set of...

The Broad Institute has a really nice set of presentations - BROAD Analyser Bootcamp - very nice tips tricks and hints...
...
Forum: Bioinformatics 10-24-2012, 05:34 AM
Replies: 4
Views: 1,400
Posted By protist
Here is info for PC - is pre 7 but try and see...

Here is info for PC - is pre 7 but try and see if you can use it...
To increase the memory allocation, create a shortcut for the Artemis program and right click on the shortcut icon. In the box...
Forum: Bioinformatics 10-24-2012, 03:14 AM
Replies: 4
Views: 1,400
Posted By protist
For increasing memory edit the info.plist file in...

For increasing memory edit the info.plist file in the Artemis folder. The protocol I use is for a mac but is as follows:

Artemis Memory Increase:
Open Terminal and go to Artemis in Applications...
Forum: Sample Prep / Library Generation 10-18-2012, 09:52 AM
Replies: 7
Views: 2,120
Posted By protist
We too have used a Biorupter for many gDNA...

We too have used a Biorupter for many gDNA libraries including DNAs from organisms with high GC content and have not seen any positional bias. I agree that the enrichment step may be the problem area
Forum: Sample Prep / Library Generation 09-27-2012, 01:58 AM
Replies: 12
Views: 14,194
Posted By protist
No Nextera kit per se but there is an application...

No Nextera kit per se but there is an application note from 2010 - Application of Nextera™ technology to RNA-seq library preparation. Nature Methods 7 (2010)
Forum: Illumina/Solexa 09-26-2012, 01:48 AM
Replies: 5
Views: 2,075
Posted By protist
Hi, we've done many fragmentations with our...

Hi, we've done many fragmentations with our Biorupter and have found the best parameters are 30sec ON/30sec OFF on high power. Make sure the bath is filled with water-ice mix. I usually do 15 min...
Forum: Literature Watch 09-25-2012, 09:13 AM
Replies: 3
Views: 2,771
Posted By protist
Brief Bioinform. 2012 Sep 17. [Epub ahead of...

Brief Bioinform. 2012 Sep 17. [Epub ahead of print]
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.
Dillies MA, Rau A, Aubert J,...
Forum: Sample Prep / Library Generation 09-19-2012, 02:32 AM
Replies: 17
Views: 10,733
Posted By protist
I would recommend RNA Zymo Clean and concentrate...

I would recommend RNA Zymo Clean and concentrate columns (5ug) we use them instead of precipitations in our library protocols.
Forum: Illumina/Solexa 09-10-2012, 02:03 AM
Replies: 8
Views: 1,528
Posted By protist
We also freeze ours and on occasion I have gone...

We also freeze ours and on occasion I have gone back an reused them for another flowcell.
Forum: Illumina/Solexa 08-27-2012, 05:07 AM
Replies: 9
Views: 5,094
Posted By protist
I would recommend Qubit HS DNA, nano drop is...

I would recommend Qubit HS DNA, nano drop is unreliable for library quantification. We routinely make our 10 nM dilutions from Qubit ng/uL values and library peak sizing (from Agilent HS DNA chips or...
Forum: Sample Prep / Library Generation 08-20-2012, 03:04 AM
Replies: 3
Views: 5,048
Posted By protist
Hi Sean, In a previous lab I frequently used...

Hi Sean,

In a previous lab I frequently used LPA for low conc RNA precipitations of tRNA substrates and it worked very well - see old paper attached for comparison of carriers for precipitation....
Forum: Sample Prep / Library Generation 08-02-2012, 07:01 AM
Replies: 18
Views: 3,114
Posted By protist
We had a set of samples that were not properly...

We had a set of samples that were not properly DNased and the DNA carried through the library prep and was identified when we mapped the reads and found both genome and transcription coverage. My...
Forum: Sample Prep / Library Generation 08-02-2012, 01:42 AM
Replies: 10
Views: 2,998
Posted By protist
MGineste, out of interest have you tried a...

MGineste, out of interest have you tried a performance test Biorupter. See http://www.unisonics.com.au/ultrasonic-equipment-performance-test.asp or seqAnswers thread...
Forum: Sample Prep / Library Generation 08-02-2012, 01:34 AM
Replies: 18
Views: 3,114
Posted By protist
So now what should I do if I want to make mRNA...

So now what should I do if I want to make mRNA libraries by standard Illumina protocol? Just go ahead with oligo-dT dynabeads? DNAse-treat? Something else?

Thanks![/QUOTE]

My advice would be...
Forum: Bioinformatics 07-31-2012, 12:30 PM
Replies: 4
Views: 1,565
Posted By protist
Yes a google search will give you the basics and...

Yes a google search will give you the basics and further reading will reveal that bacterial polyA transcripts are more often than not destined for degradation. The marker for bacterial mRNA is the...
Forum: Illumina/Solexa 07-31-2012, 08:55 AM
Replies: 2
Views: 945
Posted By protist
Are you sure they are not mitochondrial...

Are you sure they are not mitochondrial transcripts. It depends on the organism that you are working with but various euks polyadenylate both nuclear and mitochondrially derived transcripts - with...
Showing results 1 to 25 of 101

 


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