Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cufflinks 2.0.2 segmentation fault on long fragments plger RNA Sequencing 3 01-06-2015 03:41 PM
Capturing >60nt fragments smarajit Sample Prep / Library Generation 5 02-15-2013 09:50 AM
Comparison of sequence capturing polyhedron General 4 06-20-2012 07:31 AM
PubMed: Solution hybrid selection with ultra-long oligonucleotides for massively para Newsbot! Literature Watch 0 02-03-2009 06:00 AM

Thread Tools
Old 11-04-2015, 11:20 PM   #1
Junior Member
Location: NL

Join Date: Nov 2015
Posts: 1
Default ultra long fragments capturing

Is it possible to capture ultra long fragments, for example >200kb. For this I need to extract High molecular weight DNA from Human blood. But then I want to capture these long fragments for example chromosome 6 short arm or a specific 200k fragment, Hopefully there is a technique without PCR.

Anybody has experience with this?
Thuur is offline   Reply With Quote
Old 06-19-2019, 01:34 AM   #2
Junior Member
Location: china

Join Date: Aug 2017
Posts: 1

Hi,have you successfully captured ultra long fragments? Recently I want to capture a 200kb fragment from high molecular weight DNA. I wonder if you have any successful experience.
tangjj is offline   Reply With Quote
Old 06-21-2019, 07:44 AM   #3
Senior Member
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317

Old school method involved embedding cells in agarose and lysing/prepping the DNA in situ. Initially these were just little slabs of agarose. But later moved more to higher surface area collects of agarose "beads".
Anyway, then they get run on a pulsed field gel for size selection.
Anyone using agarose for their large fragment preps these days?

pmiguel is offline   Reply With Quote
Old 06-27-2019, 11:05 AM   #4
Junior Member
Location: USA, NC

Join Date: Apr 2019
Posts: 6
Smile BioNano

I agree with Phillip. Use the agarose plugs for the lysis. It might be old school, but it is making a comeback! You can use the BioNano protocol for high MW DNA. It's one of the best protocols around.

Or you can do your own homebrew version with agarose plugs.
JTH-Genome is offline   Reply With Quote
Old 05-29-2020, 08:44 PM   #5
Location: philly

Join Date: Oct 2010
Posts: 17
I think this is the best method for your purpose.
ychang is offline   Reply With Quote
Old 06-01-2020, 09:41 AM   #6
Senior Member
Location: Utah

Join Date: Mar 2010
Posts: 166

There are a couple of options. The first is the SageHLS (suggested by ychang, above)
The second is CAS9-targeted sequencing on the MinION. If you don't have a SageHLS, or know someone nearby with one, this might be the better option, as the SageHLS requires fresh cells to start, and shipping them to someone to do the capture might be a challenge. If you can access a SageHLS, that's probably a better way to try first.
ajthomas is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:31 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO