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AcronymPubMed countYearPubMed [Title] countYearTypeTitleJournalLinkDescription

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3’-end-seq

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3C-seq

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4C-seq

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5C-seq

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ALEXA-Seq12010MethodAlternative expression analysis by RNA sequencing.Nat Methods. 2010 Oct;7(10):843-7.http://dx.doi.org/10.1038/nmeth.1503

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Apopto-Seq2010MethodPresented at a meeting in 2010, analysis of Apoptotic ladders by sequencing

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AutoMeDip-Seq12010MethodAutoMeDIP-seq: a high-throughput, whole genome, DNA methylation assay.Methods. 2010 Nov;52(3):223-31.http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20385236/?tool=pubmed

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Bind-n-Seq12009MethodBind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.Nucleic Acids Res. 2009 Dec;37(22):e151.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794170/?tool=pubmed

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Bisulfite-Seq312008AnalysisShotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.Nature. 2008 Mar 13;452(7184):215-9. Epub 2008 Feb 17.http://dx.doi.org/10.1038/nature06745

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BSR-seq

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ChIA-PET http://en.wikipedia.org/wiki/ChIA-PET

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ChIP-Seq3951112007MethodGenome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.Nat Methods. 2007 Aug;4(8):651-7.http://dx.doi.org/10.1038/nmeth1068

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ClIP-Seq822009MethodAn RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.Nat Struct Mol Biol. 2009 Feb;16(2):130-7http://dx.doi.org/10.1038/nsmb.1545A method for RNA-protein interaction analysis, using RNA:protein crosslinking, followed by immunoprecipitation with antibodies for a target protein, fragmentation and high-throughput sequencing. See also RIP-Seq and HITS-CLIP

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CNV-Seq12009AnalysisCNV-seq, a new method to detect copy number variation using high-throughput sequencing.BMC Bioinformatics. 2009 Mar 6;10:80.http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19267900/?tool=pubmed

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Degradome-seq or "PARE" (without a -seq):Method: http://www.nature.com/nprot/journal/v4/n3/full/nprot.2009.8.htmlhttp://www.sciencedirect.com/science/article/pii/S0092867411007677 http://en.wikipedia.org/wiki/Degradome_sequencing

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DGE-Seq92009Method3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.BMC Genomics. 2009 Nov 16;10:531.http://www.biomedcentral.com/1471-2164/10/531

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DNA-Seq12011AnalysisZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.Genome Biol. 2011 Jul 25;12(7):R67.http://genomebiology.com/content/12/7/R67

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DNase-Seq12010MethodDNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384.http://cshprotocols.cshlp.org/cgi/pmidlookup?view=long&pmid=20150147

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dRNA-Seq22010MethodThe primary transcriptome of the major human pathogen Helicobacter pylorihttp://www.nature.com/nature/journal/v464/n7286/abs/nature08756.html dRNA-seq, differential RNA-seq

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F-Seq12008MethodF-Seq: a feature density estimator for high-throughput sequence tags.Bioinformatics. 2008 Nov 1;24(21):2537-8.http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18784119/?tool=pubmed

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FAIRE-seq

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FRT-Seq12010MethodFRT-seq: amplification-free, strand-specific transcriptome sequencing.Nat Methods. 2010 Feb;7(2):130-2.http://dx.doi.org/10.1038/nmeth.1417

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HITS-CLIP22011MethodiCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.J Vis Exp. 2011 Apr 30;(50). pii: 2638. doi: 10.3791/2638.http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21559008/?tool=pubmedSimilar to ClIP-Seq. A method for RNA-protein interaction analysis, using RNA:protein crosslinking, followed by immunoprecipitation with antibodies for a target protein, fragmentation and high-throughput sequencing

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Immune-Seq

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indel-Seq422007Methodindel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.Mol Biol Evol. 2007 Mar;24(3):640-9.http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=17158778

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IS-seq

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m6A-seq

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MBD-Seq312010MethodWhole genome DNA methylation analysis based on high throughput sequencing technology.Methods. 2010 Nov;52(3):203-12.http://linkinghub.elsevier.com/retrieve/pii/S1046-2023(10)00127-1methyl-binding protein (MBD-seq

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MeDIP-Seq72008MethodA Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.Nat Biotechnol. 2008 Jul;26(7):779-85.http://dx.doi.org/10.1038/nbt1414

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MethylCap-Seq12010MethodWhole-genome DNA methylation profiling using MethylCap-seq.Methods. 2010 Nov;52(3):232-6.http://linkinghub.elsevier.com/retrieve/pii/S1046-2023(10)00166-0

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microRNA-Seq12011MethodmicroRNA-Seq reveals cocaine-regulated expression of striatal microRNAs.RNA. 2011 Aug;17(8):1529-43.http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=21708909

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MNase-seq

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mRNA-Seq3192008MethodHighly integrated single-base resolution maps of the epigenome in Arabidopsis.Cell. 2008 May 2;133(3):523-36.http://linkinghub.elsevier.com/retrieve/pii/S0092-8674(08)00448-0

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NA-Seq12009MethodNA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.Dev Cell. 2009 Mar;16(3):466-81.http://linkinghub.elsevier.com/retrieve/pii/S1534-5807(09)00076-8

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Nascent-seq

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NET-Seq12011MethodNascent transcript sequencing visualizes transcription at nucleotide resolutionhttp://www.nature.com/nature/journal/v469/n7330/full/nature09652.htmlNET-seq, nascent transcript sequencing

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NOMe-seqhttp://hmg.oxfordjournals.org/content/early/2011/08/24/hmg.ddr356.abstract

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NSR-Seq12011MethodNSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.J Clin Invest. 2011 Mar 1;121(3):1119-29.http://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21317536/?tool=pubmedRNA sequencing, using not-so-random (NSR) primers to successfully exclude human ribosomal RNA and globin transcripts and enrich for clinical isolates of P. falciparum parasite transcripts

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oxBS-seq

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PAS-Seq12011MethodComplex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq.RNA. 2011 Apr;17(4):761-72.http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=21343387Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level

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Peak-SeqMethod

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PhIP-Seq (Phage immunoprecipitation sequencing)

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Pool-seq

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QIS-seq

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ReChIP-SeqMethod

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RIP-Seq32010MethodGenome-wide identification of polycomb-associated RNAs by RIP-seq.Mol Cell. 2010 Dec 22;40(6):939-53.http://linkinghub.elsevier.com/retrieve/pii/S1097-2765(10)00967-6Similar to ClIP-Seq. A method for RNA-protein interaction analysis, using RNA:protein crosslinking, followed by immunoprecipitation with antibodies for a target protein, fragmentation and high-throughput sequencing

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RNA-Seq3661342008MethodAnnotating genomes with massive-scale RNA sequencing.Genome Biol. 2008;9(12):R175.http://genomebiology.com/content/9/12/R175

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RNASeq32010MethodGenome-scale metabolic model integrated with RNAseq data to identify metabolic states of Clostridium thermocellum.Biotechnol J. 2010 Jul;5(7):759-67.http://dx.doi.org/10.1002/biot.201000084

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rSW-Seq12010AnalysisrSW-seq: algorithm for detection of copy number alterations in deep sequencing data.BMC Bioinformatics. 2010 Aug 18;11:432.http://www.biomedcentral.com/1471-2105/11/432method for identification of copy number alterations in a tumor genome compared to its matched control, based on application of Smith-Waterman algorithm to single-end sequencing data

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SAGE-Seq12010MethodGene expression profiling of human breast tissue samples using SAGE-Seq.Genome Res. 2010 Dec;20(12):1730-9.http://www.genome.org/cgi/pmidlookup?view=long&pmid=21045080

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Seq-Array

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Shape-seq

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Sono-Seq12009MethodMapping accessible chromatin regions using Sono-Seq.Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31.http://www.pnas.org/cgi/pmidlookup?view=long&pmid=19706456sonication of cross-linked chromatin, when combined with a size-selection step and massively parallel short-read sequencing, can be used as a method (Sono-Seq) to map locations of high chromatin accessibility in promoter regions

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SpliceSeq

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TAB-seq

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Tn-Seq32009MethodTn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms.Nat Methods. 2009 Oct;6(10):767-72.http://dx.doi.org/10.1038/nmeth.1377