title: In silico identification of novel endo-siRNAs.
abstract: Many classes of small noncoding RNAs (sncRNAs), such as microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), have been identified as important regulators of gene expression. Endo-siRNAs represent an integral part of the endogenous RNAi pathway and have been identified in multiple organisms and cell types. Wide adoption of the next-generation deep sequencing (NGS)-based sncRNA profiling has made the identification of novel sncRNA species more accessible. However, it remains a challenge to identify novel endo-siRNAs that are not collected in the current endo-siRNA databases. We have developed an in silico method for identification of novel endo-siRNAs using small RNA NGS data. Here, we describe our protocol in detail.
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, MS575, 1664 North Virginia Street, Reno, NV, 89557, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Schuster
authors.forename: Grant W
authors.initials: GW
authors.lastname: Hennig
authors.forename: Nicole
authors.initials: N
authors.lastname: Ortogero
authors.forename: Dickson
authors.initials: D
authors.lastname: Luong
authors.forename: Wei
authors.initials: W
authors.lastname: Yan
mesh_terms: D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D066264:Datasets as Topic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010944:Plants / Q000235:genetics; D034622:RNA Interference; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics*; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D012984:Software
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D034741:RNA, Small Interfering