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Related Experiment Video

Updated: Jan 16, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

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Pore-Based RNA Evaluation for Control of Integrity, Sequence, and Errors - Quality Control (PRECISE-QC).

Yvonne Yee1, Dinara Boyko2, Bhoomika Pandit3

  • 1Department of Chemical Engineering, Northeastern University, Boston, MA.

Biorxiv : the Preprint Server for Biology
|September 26, 2025
PubMed
Summary

A new quality control method using direct RNA sequencing improves synthetic RNA production. This technique enhances RNA fidelity and yield, crucial for therapeutics and gene editing applications.

Keywords:
Nanopore SequencingQuality ControlRNA ModificationsRNA synthesisSolid phase synthesis

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Genomics

Background:

  • RNA therapeutics and gene editing are rapidly advancing.
  • Current RNA synthesis methods are costly, low-yield, and produce significant byproducts.
  • Existing analytical techniques offer limited quality control for synthetic RNA, especially for longer sequences.

Purpose of the Study:

  • To develop a standardized quality control metric for synthetic RNA.
  • To enable direct insight into RNA length, sequence accuracy, and modification sites.
  • To identify and rectify errors in RNA synthesis for improved fidelity and yield.

Main Methods:

  • Utilized Oxford Nanopore direct RNA sequencing for RNA analysis.
  • Developed a computational pipeline to analyze sequencing data.
  • Applied the method to assess CRISPR guide RNAs.

Main Results:

  • The developed method provides direct insight into RNA length distribution, sequence integrity, and modification presence.
  • Identified error-prone synthesis regions and truncation sites.
  • Successfully produced and assessed high-fidelity CRISPR guide RNAs with enhanced cleavage activity.
  • Demonstrated reliable detection of RNA modifications.

Conclusions:

  • Direct RNA sequencing offers a powerful tool for synthetic RNA quality control.
  • The developed pipeline can identify and guide repair of synthesis errors.
  • This approach is crucial for improving the accuracy, integrity, and yield of synthetic RNAs for therapeutic and research applications.