Ideas for shearing and/or size-selected FFPE DNA?

durandg · 05-15-2012, 09:40 AM

Hello,

I want to perform exome sequencing on a SOLID 5500 with DNA extracted from FFPE.

After a Bioanalyzer run, i've seen -of course- a range of sizes up to Kb.
Even with doing a shearing and a size selection using the standard protocol of Library prep (Life Tech), i select sizes that are bigger that what i usually get, and actually too long to perform a correct run, for sure.

Does anyone have an idea of bead ratios to use or any program for the Covaris S220 to shear efficiently that kind of degraded DNA

All help will be appreciated :-)

Regards,

Durandg.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Shearing of FFPE extracted DNA.	durandg	General	4	07-08-2013 06:41 AM
Problem with BWA mapping of Illumina PE short insert size fragments (FFPE material)	LadyGray	Bioinformatics	2	10-22-2012 02:20 AM
FFPE DNA next gen sequencing	han526	Introductions	0	04-27-2012 07:23 AM
FFPE DNA prep from LCM	PamPetrel	Sample Prep / Library Generation	1	06-08-2011 01:41 AM
New! Ovation WGA FFPE and RNA-Seq FFPE workflow solutions from NuGEN Technologies	NuGEN	Vendor Forum	0	11-03-2010 10:02 AM

05-15-2012, 09:40 AM	#1
durandg Member Location: Lyon, France Join Date: May 2012 Posts: 12	Ideas for shearing and/or size-selected FFPE DNA? Hello, I want to perform exome sequencing on a SOLID 5500 with DNA extracted from FFPE. After a Bioanalyzer run, i've seen -of course- a range of sizes up to Kb. Even with doing a shearing and a size selection using the standard protocol of Library prep (Life Tech), i select sizes that are bigger that what i usually get, and actually too long to perform a correct run, for sure. Does anyone have an idea of bead ratios to use or any program for the Covaris S220 to shear efficiently that kind of degraded DNA All help will be appreciated :-) Regards, Durandg.