SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
Library prep with <100ng DNA? sstarkenburg Illumina/Solexa 20 03-05-2013 04:25 AM
Single stranded molecules run crazy slow on a DNA Agilent Chip pmiguel Sample Prep / Library Generation 14 03-19-2012 10:13 AM
single stranded DNA ChIP-Seq using Solexa litd Illumina/Solexa 3 05-27-2011 01:42 AM
Single stranded coverage from sam/bam ewilbanks Bioinformatics 2 05-13-2011 11:13 PM
Library prep using chromosome sorted DNA Scotch Sample Prep / Library Generation 0 08-14-2010 04:44 PM

Reply
 
Thread Tools
Old 11-03-2010, 10:15 AM   #1
genlyai
Member
 
Location: Boston, MA

Join Date: Aug 2009
Posts: 39
Default Library prep from single-stranded DNA?

Hi everyone,

For an application I'm interested in, I would like to sequence libraries on Illumina (or Solid, I guess) starting from material containing both double and single-stranded DNA. If I'm not mistaken, standard library construction will miss single-stranded DNA, right?

Is anyone aware of a way to get single- and double- (or at least single- alone) stranded material represented in a library?

Thanks very much for your help!
genlyai is offline   Reply With Quote
Old 11-04-2010, 09:16 AM   #2
upendra_35
Senior Member
 
Location: USA

Join Date: Apr 2010
Posts: 102
Default

Please refer this paper for more on strand specific sequencing
http://genome.cshlp.org/content/earl...8.109.full.pdf
upendra_35 is offline   Reply With Quote
Old 11-05-2010, 07:14 AM   #3
josdegraaf
Member
 
Location: Germany

Join Date: Mar 2010
Posts: 33
Default

http://www.ncbi.nlm.nih.gov/pubmed/19815668
josdegraaf is offline   Reply With Quote
Old 11-12-2010, 12:26 PM   #4
genlyai
Member
 
Location: Boston, MA

Join Date: Aug 2009
Posts: 39
Default

Thanks to both of you. To clarify, I'm not interested in strand-specific information, as such, but just in generating libraries that would include DNA that starts off as single-stranded.

Upendra, I'm not sure I see how the paper you posted will help, but maybe I'm just missing it.

Jos, your reference claims that single-stranded cDNA will make it into a library even if you don't do anything special. The proposed mechanism is through poorly complementary double-stranded regions being processed to ligatable ends during the blunting step. This might well be useful to me, but the paper lacks info about how efficient the process is and what biases it introduces. Does anyone have any insight into this?
genlyai is offline   Reply With Quote
Reply

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 12:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO