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In Silico Identification of Novel Endo-siRNAs

  • Andrew Schuster
  • Grant W. Hennig
  • Nicole Ortogero
  • Dickson Luong
  • Wei YanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1218)

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.

Key words

Noncoding RNA Endogenous small interference RNA Next-generation sequencing RNA-Seq Annotation 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Andrew Schuster
    • 1
  • Grant W. Hennig
    • 1
  • Nicole Ortogero
    • 1
  • Dickson Luong
    • 1
  • Wei Yan
    • 1
    Email author
  1. 1.Department of Physiology and Cell BiologyUniversity of Nevada School of MedicineRenoUSA

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