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Related Experiment Video

Updated: Jan 2, 2026

Identification of Circular RNAs using RNA Sequencing
08:25

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

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Identification of Circular RNAs using RNA Sequencing.

Shobana Sekar1, Philipp Geiger1, Lori Cuyugan1

  • 1Translational Genomic Research Institute; Arizona Alzheimer's Consortium.

Journal of Visualized Experiments : Jove
|December 3, 2019
PubMed
Summary
This summary is machine-generated.

Optimizing circular RNA (circRNA) detection involves specific library preparation. A stranded total RNA kit with RNase R treatment and 4 µg input best identifies circRNAs, with brain tissues showing highest abundance.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Circular RNAs (circRNAs) are non-coding RNAs with diverse regulatory functions.
  • Traditional RNA sequencing methods often miss circRNAs due to library preparation biases.
  • Accurate circRNA detection is crucial for understanding their biological roles.

Purpose of the Study:

  • To optimize a library construction protocol for enhanced circRNA detection.
  • To compare different RNA library preparation kits, pre-treatment methods, and RNA input amounts.
  • To evaluate circRNA abundance across various human tissue types.

Main Methods:

  • Systematic comparison of two whole transcriptome library kits with and without RNase R pre-treatment.
  • Testing variable total RNA input amounts (1–4 µg).
  • Analysis of RNA-seq data using six distinct circRNA detection tools across multiple tissue and brain regions.

Main Results:

  • A stranded total RNA library preparation kit combined with RNase R pre-treatment and 4 µg of total RNA input yielded the highest number of identified circRNAs.
  • Brain tissues exhibited a higher enrichment of circRNAs compared to other tested tissues.
  • Optimization significantly improved circRNA identification rates.

Conclusions:

  • The optimized protocol enhances the identification of circRNAs, overcoming limitations of standard RNA-seq.
  • RNase R pre-treatment and specific library kits are critical for circRNA discovery.
  • Tissue-specific differences in circRNA abundance, particularly in brain tissue, warrant further investigation.