single stranded DNA ChIP-Seq using Solexa

[litd]

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]

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/v7/n2/full/nmeth.1417.html

Or modify the mRNA/small RNA kit to make the libs.

[sridharacharya]

single stranded DNA sequencing

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/v7/n2/full/nmeth.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]

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...