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Forum: Illumina/Solexa 07-29-2016, 07:49 AM
Replies: 14
Views: 4,760
Posted By subxero
Is this the only solution you tried, increasing...

Is this the only solution you tried, increasing the input?

We are having this problem right now but we have very limited amounts of RNA so are hands are a bit tied as far as the amount of input...
Forum: RNA Sequencing 02-04-2016, 08:50 AM
Replies: 1
Views: 1,285
Posted By subxero
High % of reads with multiple alignments

Recently mapped some RNAseq reads with Tophat that were prepped from human whole blood, globin cleared, then prepped with Illumina Total stranded RNA with ribo zero gold (rRNA reduction and globin...
Forum: Sample Prep / Library Generation 10-01-2015, 05:20 AM
Replies: 16
Views: 9,812
Posted By subxero
it's pointed out in another thread somewhere but...

it's pointed out in another thread somewhere but if you are switching between the 2 kits you need to do some comparison tests of your samples using each kit. BR tends to give a higher reading by a...
Forum: Clinical Sequencing 05-02-2014, 10:48 AM
Replies: 0
Views: 7,647
Posted By subxero
Any labs go from non-clinical to clinical?

Anyone one develop their research lab to be able to do clinical sequencing? And more specifically with the MiSeq?

We are interested in the idea and trying to figure out what would need to be done...
Forum: Illumina/Solexa 01-08-2014, 11:10 AM
Replies: 3
Views: 1,485
Posted By subxero
the libraries were all prepped the same day with...

the libraries were all prepped the same day with same protocol in same lot, so they should all be quite similar in size
Forum: Illumina/Solexa 01-08-2014, 10:17 AM
Replies: 3
Views: 1,485
Posted By subxero
problem with pooled library cluster generation MiSeq

When pooling 8 TruSeq RNA libraries together for a 50 cycle QC run on the MiSeq I am having a problem in that my libraries do not cluster equally.

I have 2 libraries that both account for ~40% of...
Forum: Sample Prep / Library Generation 11-06-2013, 07:14 AM
Replies: 2
Views: 1,434
Posted By subxero
^please excuse my typo in thread topic :o

^please excuse my typo in thread topic :o
Forum: Sample Prep / Library Generation 11-06-2013, 05:57 AM
Replies: 2
Views: 1,434
Posted By subxero
Looking for optamized globinclear protocol

I was wondering if any one has a good Globin reduction protocol for human RNA they are willing to share?

We currently use the LifeTech GLOBINclear kit and it works well but calls for 1.5ug of RNA...
Forum: Sample Prep / Library Generation 09-27-2013, 10:02 AM
Replies: 8
Views: 3,383
Posted By subxero
Here is a trace from my latest library prep. I...

Here is a trace from my latest library prep. I ran these libraries on a DNA 1000 chip instead of the HS chip as I figured had enough library to do so.

I still need to do the kappa qPCR QC to get...
Forum: Sample Prep / Library Generation 09-27-2013, 07:12 AM
Replies: 3
Views: 3,372
Posted By subxero
The size selection looks off, I have had over...

The size selection looks off, I have had over amplification and it does not look like that.
Forum: Illumina/Solexa 09-13-2013, 05:54 AM
Replies: 1
Views: 2,745
Posted By subxero
HiSeq MiSeq library compatibility ?

I am looking to run some libraries I initially prepped for HiSeq via Trueseq RNA V2 on the MiSeq and have a question.

So I have read that the protocols are compatible, but the MiSeq only does PE...
Forum: Sample Prep / Library Generation 09-05-2013, 06:54 AM
Replies: 8
Views: 3,383
Posted By subxero
cluster with cbot then run on HiSeq2000 I...

cluster with cbot then run on HiSeq2000

I guess the big question is, what do I have to do to get this library to a point where it can be sequenced efficiently?

A) get ride of dimers
B)...
Forum: Sample Prep / Library Generation 09-05-2013, 05:10 AM
Replies: 8
Views: 3,383
Posted By subxero
Ill definitely look into another bead clean up...

Ill definitely look into another bead clean up step.

how much total library should I be aiming for in the end?
Forum: Sample Prep / Library Generation 09-03-2013, 12:21 PM
Replies: 8
Views: 3,383
Posted By subxero
Yeah there was a PCR step to amplify the Library,...

Yeah there was a PCR step to amplify the Library, I figured I had over amplification but still don't understand how my samples are over amplified yet the samples prepped a few weeks prior using all...
Forum: Sample Prep / Library Generation 09-03-2013, 10:13 AM
Replies: 8
Views: 3,383
Posted By subxero
BA Traces what's going on?

Quick summary,

some library prepped using truseq RNA v2 kit slightly modified protocol (mainly volumes)

Samples 1-8 are library I prepped last week (my first time), some samples at different...
Forum: Illumina/Solexa 08-02-2013, 06:09 AM
Replies: 3
Views: 3,554
Posted By subxero
I would like to bring this thread back from the...

I would like to bring this thread back from the dead.

Any other kits out there that are comparable or better than the TruSeq RNA kits?

If so and you have experience with the said kit could you...
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