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Genome-Wide circRNA Profiling from RNA-seq Data

  • Daphne A. Cooper
  • Mariela Cortés-López
  • Pedro Miura
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1724)

Abstract

The genome-wide expression patterns of circular RNAs (circRNAs) are of increasing interest for their potential roles in normal cellular homeostasis, development, and disease. Thousands of circRNAs have been annotated from various species in recent years. Analysis of publically available or user-generated rRNA-depleted total RNA-seq data can be performed to uncover new circRNA expression trends. Here we provide a primer for profiling circRNAs from RNA-seq datasets. The description is tailored for the wet lab scientist with limited or no experience in analyzing RNA-seq data. We begin by describing how to access and interpret circRNA annotations. Next, we cover converting circRNA annotations into junction sequences that are used as scaffolds to align RNA-seq reads. Lastly, we visit quantifying circRNA expression trends from the alignment data.

Key words

circRNA Circular RNAs Expression analysis Ribo-depleted total RNA-seq 

Notes

Acknowledgments

This work was supported by the National Institute of General Medical Sciences grant P20 GM103650 and National Institute on Aging grant R15 AG052931. We would also like to thank Matthew Bauer and David Knupp for critical review of this chapter.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Department of BiologyUniversity of Nevada, RenoRenoUSA

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