The list at the bottom is occasionally edited to include new methods.
There is an ever increasing number of next generation sequencing acronyms (see the link to a table at the bottom of this post), other than the commonly used ChIP-Seq and RNA-Seq most have been used only once in the article where the acronym was first used. I suspect authors are trying to come up with something as catchy as "ChIP-Seq" in the ope that their paper will be cited more frequently. A search through PubMed suggests otherwise.
My list contains just over 30 acronyms presented in papers, posters or meetings over the past few years. A search for these in PubMed brings up almost 850 papers. RNA-Seq (including mRNA-Seq or RNASeq) account for 48%, ChIP-Seq has 47%, ClIP-Seq (including RIP-Seq and HITS-ClIP) has 2%, about 1% of papers are versions of methylation sequencing.
The 2007 ChIP-Seq paper "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing" in Nat Methods started this sequencing acronym name game. However this has been played out before with other technologies.
I am certain I will have missed a few out so feel free to comment and I'll upadte the tabel with this information in it. I'd also like to ask authors and editors to strongly consider adding any more to this list unless there is a strongly compelling reason.
Here's my list: ALEXA-Seq, Apopto-Seq, AutoMeDip-Seq, Bind-n-Seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq, ChiRP-seq, ClIP-Seq, CNV-Seq, Degradome-seq, DGE-Seq, DNA-Seq, DNase-Seq, dRNA-Seq, F-Seq, FAIRE-seq, FRT-Seq, HITS-CLIP, Immune-Seq, indel-Seq, MBD-Seq, MeDIP-Seq, MethylCap-Seq, microRNA-Seq, mRNA-Seq, NA-Seq, NET-Seq, NOMe-seq, NSR-Seq, PAS-Seq, Peak-Seq, PhIP-Seq, Protein-seq, ReChIP-Seq, RIP-Seq, RIT-seq, RNA-Seq, RNASeq, rSW-Seq, SAGE-Seq, Seq-Array, Sono-Seq, Sort-seq, Tn-Seq.
Others added by you: (now all moved to the list above)
One comment suggested I should have labeled the post as "Sequencing abbreviations". Having now taken the time to look at what the difference is between an acronym and an abbreviation, I think there is a bit of both here so I'll leave it for now.
Here's the data...