single stranded DNA ChIP-Seq using Solexa

litd · 05-13-2010, 09:21 PM

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

Nik · 05-18-2010, 11:23 AM

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.

sridharacharya · 05-26-2011, 12:59 PM

Quote:

Originally Posted by Nik

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?

protist · 05-27-2011, 02:42 AM

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...

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05-13-2010, 09:21 PM	#1
litd Member Location: US Join Date: Mar 2010 Posts: 14	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

05-18-2010, 11:23 AM	#2
Nik Member Location: London Join Date: May 2009 Posts: 14	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.

05-27-2011, 02:42 AM	#4
protist Senior Member Location: Ireland Join Date: Jan 2009 Posts: 101	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...