Transcriptomewide survey of pseudorabies virus using next-A nd third-generation sequencing platforms

Dóra Tombácz, Donald Sharon, Attila Szûcs, Norbert Moldován, Michael Snyder, Z. Boldogkői

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Pseudorabies virus (PRV) is an alphaherpesvirus of swine. PRV has a large double-stranded DNA genome and, as the latest investigations have revealed, a very complex transcriptome. Here, we present a large RNA-Seq dataset, derived from both short-A nd long-read sequencing. The dataset contains 1.3 million 100 bp paired-end reads that were obtained from the Illumina random-primed libraries, as well as 10 million 50 bp single-end reads generated by the Illumina polyA-seq. The Pacific Biosciences RSII non-amplified method yielded 57,021 reads of inserts (ROIs) aligned to the viral genome, the amplified method resulted in 158,396 PRV-specific ROIs, while we obtained 12,555 ROIs using the Sequel platform. The Oxford Nanopore's MinION device generated 44,006 reads using their regular cDNA-sequencing method, whereas 29,832 and 120,394 reads were produced by using the direct RNA-sequencing and the Cap-selection protocols, respectively. The raw reads were aligned to the PRV reference genome (KJ717942.1). Our provided dataset can be used to compare different sequencing approaches, library preparation methods, as well as for validation and testing bioinformatic pipelines.

Original languageEnglish
Article number180119
JournalScientific data
Volume5
DOIs
Publication statusPublished - Jun 19 2018

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third generation
Viruses
Sequencing
Virus
Genome
Genes
RNA
Nanopore
Nanopores
Bioinformatics
CDNA
Preparation
DNA
Pipelines
Testing
Pseudorabies virus
Libraries

ASJC Scopus subject areas

  • Statistics and Probability
  • Information Systems
  • Education
  • Computer Science Applications
  • Statistics, Probability and Uncertainty
  • Library and Information Sciences

Cite this

Transcriptomewide survey of pseudorabies virus using next-A nd third-generation sequencing platforms. / Tombácz, Dóra; Sharon, Donald; Szûcs, Attila; Moldován, Norbert; Snyder, Michael; Boldogkői, Z.

In: Scientific data, Vol. 5, 180119, 19.06.2018.

Research output: Contribution to journalArticle

Tombácz, Dóra ; Sharon, Donald ; Szûcs, Attila ; Moldován, Norbert ; Snyder, Michael ; Boldogkői, Z. / Transcriptomewide survey of pseudorabies virus using next-A nd third-generation sequencing platforms. In: Scientific data. 2018 ; Vol. 5.
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