SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
ChIP-Seq: Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Newsbot! Literature Watch 19 02-29-2016 08:08 PM
Single stranded molecules run crazy slow on a DNA Agilent Chip pmiguel Sample Prep / Library Generation 14 03-19-2012 11:13 AM
ChIP-Seq: Single-tube linear DNA amplification for genome-wide studies using a few th Newsbot! Literature Watch 0 01-28-2012 03:00 AM
Single stranded coverage from sam/bam ewilbanks Bioinformatics 2 05-14-2011 12:13 AM
Library prep from single-stranded DNA? genlyai Sample Prep / Library Generation 3 11-12-2010 01:26 PM

Reply
 
Thread Tools
Old 05-13-2010, 09:21 PM   #1
litd
Member
 
Location: US

Join Date: Mar 2010
Posts: 14
Default single stranded DNA ChIP-Seq using Solexa

Hi,

we are working on a chip-seq project using antibody to pulldown damaged single stranded DNA. Is there any protocols using ssDNA for deep sequencing using Solexa?

Thanks,

litd
litd is offline   Reply With Quote
Old 05-18-2010, 11:23 AM   #2
Nik
Member
 
Location: London

Join Date: May 2009
Posts: 14
Default

Hi,

I'm not sure if you mean the actual ChIP or sequencing. If seq then you could modify this:

http://www.nature.com/nmeth/journal/...meth.1417.html

Or modify the mRNA/small RNA kit to make the libs.
Nik is offline   Reply With Quote
Old 05-26-2011, 12:59 PM   #3
sridharacharya
Member
 
Location: Institute, WV

Join Date: May 2010
Posts: 24
Question single stranded DNA sequencing

Quote:
Originally Posted by Nik View Post
Hi,

I'm not sure if you mean the actual ChIP or sequencing. If seq then you could modify this:

http://www.nature.com/nmeth/journal/...meth.1417.html

Or modify the mRNA/small RNA kit to make the libs.
I am curious about the same question as I am still not sure. Is it possible to use Illumina for sequencing single stranded DNA.
We are enriching some regions of genomic DNA by fragmentation, denaturation and hybridization to specific oligos. The single stranded DNA that is enriched needs to be sequenced. Is there any way to get sequence information of these single stranded DNA fragments?
sridharacharya is offline   Reply With Quote
Old 05-27-2011, 02:42 AM   #4
protist
Senior Member
 
Location: Ireland

Join Date: Jan 2009
Posts: 101
Default

For RNAseq single stranded cDNA can be used to construct a library. See A simple method for directional transcriptome sequencing using Illumina technology http://www.ncbi.nlm.nih.gov/pmc/arti...3/?tool=pubmed for the details.

They compared double stranded and single stranded cDNA as inputs for library prep. Your single-stranded DNA should work - however it would need to be fragmented to the correct size before end repair, A addition, adapter ligation etc...
protist 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 03:21 AM.


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