X-Seq: Can You Provide A Listing Of The Various Applications For Sequencing Technologies?

Question

[polarise]

Could we compile a growing list of all the different sequencing applications? This could be accompanied by a short description for tyros.

RNA-Seq involves sequencing of transcriptomes consisting of different species of RNA (e.g. mRNA) as cDNA. It provides a good picture of transcript abundance as well as transcript-processing events. Wikipedia page

ChIP-Seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Wikipedia page

ChIP-Exo is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to less than one base pair. It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5'-3' direction to within a small number of nucleotides of the protein binding site. Wikipedia page

miRNA-Seq Wikipedia page

DNA-Seq SEQWiki page

Methyl-Seq Wikipedia page

RAD-Seq University of Edinburgh page

GRO-Seq is the name for Global Run-On sequencing. See more details here: ngsbioinformatics.com page

NET-Seq is short for Native Elongating Transcript sequencing. It involves immunoprecipitation of RNA polymerase followed by sequencing bound RNA fragments Nature paper

FAIRE-Seq is the name for Formaldehyde-Assisted Isolation of Regulatory Elements following by sequencing. Check out a description here: Wikipedia page

Ribo-Seq consists of freezing ribosomes to capture bound mRNA in the process of translation. After the ribosomes are primed open the mRNA fragments are sequenced. Science page

Update: Here's a much better list: Lior Pachter's list of *Seq

PK

[Istvan Albert]

I would suggest that you edit the main post and add the new answers as they appear

[polarise]

Splendid idea. I'll keep an eye on this post.

Answer 1

[NextGenSeek]

Nature BioTechnology issue had this article "The expanding scope of DNA sequencing" listing NGS applications, http://www.nature.com/nbt/journal/v30/n11/full/nbt.2421.html.

(If it was behind pay wall,) we blogged this and have this list with references here

http://nextgenseek.com/2012/11/did-you-know-there-are-at-least-20-applications-of-next-generation-dna-sequencing/

[Rm]

@NextGenSeek : nice article

Answer 2

[Istvan Albert]

• ChIP-Seq: combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. For more info see:http://en.wikipedia.org/wiki/ChIP-sequencing
• ChIP-Exo: It is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to less than one base pair. It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5'-3' direction to within a small number of nucleotides of the protein binding site. For more info see:http://en.wikipedia.org/wiki/ChIP-exo

Answer 3

[Rm]

miRNA-seq

ChIP-seq

DNA-Seq

Methyl-Seq

Answer 4

[Leszek]

I came across quite unusual technique: Restriction site Associated DNA Sequencing (RAD-Seq)