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Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Transcriptome-wide analysis of a baculovirus using nanopore sequencing.

Zsolt Boldogkői1, Norbert Moldován1, Attila Szűcs1

  • 1Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary.

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|December 5, 2018
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Summary

This study presents a comprehensive dataset of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) transcripts, generated using Oxford Nanopore Technologies sequencing. The data enables detailed analysis of viral and host cell transcriptomic and epitranscriptomic patterns.

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Area of Science:

  • Molecular Biology
  • Virology
  • Genomics

Background:

  • Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a key insect pathogen and a widely used expression vector.
  • AcMNPV possesses a large double-stranded DNA genome with a complex transcriptome.
  • Understanding the AcMNPV transcriptome is crucial for its application in biotechnology.

Purpose of the Study:

  • To generate and release a comprehensive dataset of AcMNPV transcripts using long-read sequencing.
  • To provide resources for analyzing viral and host cell transcriptomic and epitranscriptomic dynamics.
  • To facilitate the validation of bioinformatics tools for transcriptomic analysis.

Main Methods:

  • Utilized Oxford Nanopore Technologies (ONT) long-read sequencing platforms.
  • Employed both cDNA and direct RNA sequencing techniques.
  • Applied a Cap-selection protocol for enhanced transcript capture and aligned reads to the AcMNPV reference genome.

Main Results:

  • Generated a large dataset including over 520,000 AcMNPV reads and 1.3 million host cell reads via cDNA sequencing.
  • Obtained thousands of reads using direct RNA sequencing and Cap-selection methods.
  • Released a static and dynamic transcript catalog for AcMNPV.

Conclusions:

  • The released dataset offers a valuable resource for in-depth transcriptomic and epitranscriptomic studies of AcMNPV and its host.
  • This data supports the development and validation of bioinformatics software for viral transcript analysis.
  • The findings contribute to a deeper understanding of baculovirus gene expression and regulation.