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Nanopore Direct RNA Sequencing of Monosome- and Polysome-Bound RNA
2023Polysome fractionation makes use of density gradients and ultracentrifugation to separate transcripts based on their specific number of bound ribosomes, and can be combined with downstream analysis such as cDNA-seq (commonly known as RNA-seq), microarray analysis, RT-qPCR, or Northern blotting.
Lan Anh Catherine, Nguyen +2 more
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RNA Modification Detection Using Nanopore Direct RNA Sequencing and nanoDoc2
2023RNA modifications regulate multiple aspects of cellular function including RNA splicing, translation, export, decay, stability, and phase separation. One of the comprehensive ways to detect such modifications is by the recent advancement of direct RNA sequencing from Oxford Nanopore Technologies (ONT).
Hiroki, Ueda +2 more
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Direct Chemical Sequencing of End-Labeled RNA
Cold Spring Harbor Protocols, 2015Chemical sequencing of RNA relies on the fact that each of the four bases in RNA is susceptible to chemical modification in a different way. In this protocol, end-labeled RNAs are subjected to base-specific chemical modification reactions that make the RNA strand adjacent to the modified base susceptible to cleavage.
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Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing
Plant Molecular Biology, 1991A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup ...
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TARDIS, a targeted RNA directional sequencing method for rare RNA discovery
Nature Protocols, 2015High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper the identification of rare transcripts contained within the RNA repertoire.
Portal, Maximiliano Moises +3 more
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Directed Deletion of a Yeast Transfer RNA Intervening Sequence
Science, 1980Many eukaryotic genes contain intervening sequences, segments of DNA that interrupt the continuity of the gene. They are removed from RNA transcripts of the gene by a process known as splicing. The intervening sequence in a yeast tyrosine transfer RNA (tRNA Tyr ) suppressor gene was deleted in order to test its role
R B, Wallace +5 more
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Direct detection of RNA repair by nanopore sequencing
2022Abstract Ligation by plant and fungal RNA ligases yields an internal 2′-phosphate group on each RNA ligation product. In budding yeast, this covalent mark occurs at the splice junction of two targets of ligation: intron-containing tRNAs and the messenger RNA HAC1 . The repertoire of
Laura K. White +3 more
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Advances in nanopore direct RNA sequencing
Nature Methods, 2022Miten Jain +3 more
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Computational methods for RNA modification detection from nanopore direct RNA sequencing data
RNA Biology, 2021Eva Maria Novoa +2 more
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