TruSeq or Nextera kit for library prep?

rooty · 05-06-2011, 06:43 AM

Hello,
Has anyone compared the TruSeq and Nextera kits for making RNA-seq libraries for Illumina HiSeq?
I am trying to make libraries from relatively small quantities of totalRNA from plant cells. I would like to know if someone has done this comparison.
Many thanks!

xinhui · 05-13-2011, 11:46 AM

Co-ask.

Thanks.

ymc · 08-03-2012, 12:20 AM

I want to know too

pmiguel · 08-03-2012, 03:28 AM

Is there a Nextera RNAseq prep kit? I don't see it on the Illumina website.
What do you mean by "relatively small quantities" of RNA.

--
Phillip

SLeigh-Brown · 09-27-2012, 12:57 AM

Hi everyone,

Illumina currently only sell a Nextera kit for DNA library preps.

The Nextera enzyme will only work on double-stranded DNA, so if you are considering testing it for RNAseq, I would recommend making double stranded cDNA first. Perhaps also consider testing the Nextera XT kit, since this is designed to work with Amplicons and very low input.

We have tested the Truseq RNA kit down to 100ng total RNA input (for RNA with a high RIN number, >8) and the data has been good. How low are you trying to go?

S

protist · 09-27-2012, 01:58 AM

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)

SageSigh · 05-20-2013, 12:06 PM

Illumina's Epicentre division has an RNA-seq kit that you may have interest in. http://www.epibio.com/products/rna-s...reparation-kit

kevin sun · 06-10-2013, 03:23 PM

what properties does the DNA polymerase have in the Truseq DNA sample prepare kit?

LVAndrews · 10-16-2013, 03:11 PM

You all should view these links. Nextera works for RNAseq with some caveats, but it has been published:

http://epicentral.blogspot.com/2010/...r-rna-seq.html

http://www.nature.com/nmeth/journal/...meth.f.317.pdf

http://genome.cshlp.org/content/earl...3.111.full.pdf

LVAndrews · 10-16-2013, 03:12 PM

Oop.. I missed the post above with the nat.meth paper.

Olaf Blue · 10-17-2013, 06:00 AM

Epicentre has a Nextera-"powered" RNA-seq Kit, called "Totalscript", good for 1-5 ng of high quality total RNA input.

http://www.epibio.com/applications/r...eq-kit?details

Not much available in the way of posters, publications or the like at this time, though.....

Olaf

dongzw · 10-29-2013, 05:34 AM

I'm also a little bit confused. Nextera kits looks great! However,since Nextera is much better than Truseq, why does Illumina still sell Truseq kits?

Olaf Blue · 10-29-2013, 06:02 AM

We can't say it's "much better", problem is that the Transposomes can't get within 20-50 bases of the end if each target (it's the biology of the system) such that coverage depth drops way off on the ends.

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05-06-2011, 06:43 AM	#1
rooty Junior Member Location: Durham, NC Join Date: Jan 2011 Posts: 1	TruSeq or Nextera kit for library prep? Hello, Has anyone compared the TruSeq and Nextera kits for making RNA-seq libraries for Illumina HiSeq? I am trying to make libraries from relatively small quantities of totalRNA from plant cells. I would like to know if someone has done this comparison. Many thanks!

09-27-2012, 12:57 AM	#5
SLeigh-Brown Junior Member Location: Cambridge, UK Join Date: Dec 2011 Posts: 3	Truseq on 100ng input Hi everyone, Illumina currently only sell a Nextera kit for DNA library preps. The Nextera enzyme will only work on double-stranded DNA, so if you are considering testing it for RNAseq, I would recommend making double stranded cDNA first. Perhaps also consider testing the Nextera XT kit, since this is designed to work with Amplicons and very low input. We have tested the Truseq RNA kit down to 100ng total RNA input (for RNA with a high RIN number, >8) and the data has been good. How low are you trying to go? S

05-13-2011, 11:46 AM	#2
xinhui Junior Member Location: OHIO Join Date: Apr 2010 Posts: 1	Co-ask. Thanks.

08-03-2012, 12:20 AM	#3
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	I want to know too

08-03-2012, 03:28 AM	#4
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,315	Is there a Nextera RNAseq prep kit? I don't see it on the Illumina website. What do you mean by "relatively small quantities" of RNA. -- Phillip

05-20-2013, 12:06 PM	#7
SageSigh Member Location: Boston, MA North Shore Join Date: Aug 2010 Posts: 12	Illumina's Epicentre division has an RNA-seq kit that you may have interest in. http://www.epibio.com/products/rna-s...reparation-kit

06-10-2013, 03:23 PM	#8
kevin sun Junior Member Location: blacksburg Join Date: Feb 2013 Posts: 1	what properties does the DNA polymerase have in the Truseq DNA sample prepare kit?

10-16-2013, 03:11 PM	#9
LVAndrews Member Location: Flagstaff, AZ Join Date: Sep 2012 Posts: 55	You all should view these links. Nextera works for RNAseq with some caveats, but it has been published: http://epicentral.blogspot.com/2010/...r-rna-seq.html http://www.nature.com/nmeth/journal/...meth.f.317.pdf http://genome.cshlp.org/content/earl...3.111.full.pdf

10-16-2013, 03:12 PM	#10
LVAndrews Member Location: Flagstaff, AZ Join Date: Sep 2012 Posts: 55	Oop.. I missed the post above with the nat.meth paper.

10-17-2013, 06:00 AM	#11
Olaf Blue Member Location: Madison, WI Join Date: Nov 2010 Posts: 58	Epicentre has a Nextera-"powered" RNA-seq Kit, called "Totalscript", good for 1-5 ng of high quality total RNA input. http://www.epibio.com/applications/r...eq-kit?details Not much available in the way of posters, publications or the like at this time, though..... Olaf

10-29-2013, 05:34 AM	#12
dongzw Junior Member Location: Shanghai Join Date: Aug 2011 Posts: 8	I'm also a little bit confused. Nextera kits looks great! However,since Nextera is much better than Truseq, why does Illumina still sell Truseq kits?

10-29-2013, 06:02 AM	#13
Olaf Blue Member Location: Madison, WI Join Date: Nov 2010 Posts: 58	We can't say it's "much better", problem is that the Transposomes can't get within 20-50 bases of the end if each target (it's the biology of the system) such that coverage depth drops way off on the ends.