Poly(A)-Tail-Primed Sequencing Poly(A)-tail-primed sequencing (2P-Seq) is designed to quantify mRNA stability and translational efficiency by characterizing 3’UTR isoforms (Spies et al., 2013). First, poly(A)+ mRNAs are isolated from total RNA and partially digested by RNase T1 to cleave the non-UTR regions. Poly (A)+ mRNA fragments […]

All of the RNA Transcription sequencing methods are collected together under this heading

Use Dimethyl Sulphate Methylation of Unprotected Adenines and Cytosines Structure-Seq profiles RNA structures for in vivo or in vitro applications with single-nucleotide resolution (Ding et al., 2014) (Ding et al., 2015). This method identifies secondary RNA structures by using the chemical modification induced by DMS […]

Specific Parallel Amplification of 5′ RNA Ends SPARE identifies genome-wide miRNA processing intermediates in plants (Schapire et al., 2013). SPARE infers the directionality of miRNA processing (base-to-loop or loop-to-base) by analyzing the resultant cDNA sequences. If only the first cleavage position is detected, the miRNA […]

Parallel Analysis of RNA Structure PARS-Seq mapping provides information about the secondary and tertiary structure of RNA (Wan et al., 2013). In this method, RNA is digested with RNases that are specific for double-stranded and single-stranded RNA, respectively. The resulting fragments are reverse-transcribed to cDNA. […]

Alkaline Phosphatase, Calf Intestine-Tobacco Acid Pyrophosphatase Sequencing CIP-TAP maps capped small RNAs (Gu et al., 2012). In this method, RNA is treated with CIP followed by 3′-end linker ligation. Next, the RNA is treated with TAP, followed by 5′-end linker ligation. The fragments are reverse-transcribed […]

CXXC Affinity Purification Plus Deep Sequencing CAP-seq maps the 5′ end of RNAs anchored to RNAPII (Illingworth et al., 2010). In this method, RNA transcripts are treated sequentially with Terminator exonuclease, CIP, and TAP, followed by linker ligation and RT to cDNA. Deep sequencing of […]

All of the RNA Structure sequencing methods are collected together under this heading

Pseudouridine Site Identification Sequencing PSI-Seq identifies RNA sequences containing pseudouridine sites using high-throughput sequencing (Lovejoy et al., 2014). PSI-Seq uses N-Cyclohexyl-N_-(2-morpholinoethyl)carbodiimide (CMC) to modify pseudouridines selectively, effectively halting reverse transcription. The cDNA libraries are prepared by the ARTseq method.Briefly, samples are poly(A)-selected, treated with DNase, […]

Method for Genome-Wide Identification of Pseudouridylation Sites Pseudo-Seq detects pseudouridylation sites in ncRNAs with single-nucleotide resolution using high-throughput sequencing (Carlile et al., 2014). Pseudo-Seq is very similar to PSI-seq, in that both methods use CMC to modify pseudouridines selectively and halt reverse transcription. However, Pseudo-Seq […]