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- and 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.
Highlights
Background & SummaryPseudorabies virus (PRV) is a causative agent of Aujeszky’s disease (AD)[1] in pigs
Viruses and infection conditions Immortalized porcine kidney-15 (PK-15; ATCC® CCL-33TM) cells were used for the propagation of pseudorabies virus strain Kaplan (PRV-Ka) at 37 °C and 5% CO2 in Dulbecco’s modified Eagle medium (DMEM, Gibco Invitrogen) supplemented with 5% foetal bovine serum (FBS; Gibco Invitrogen)
The virus stock was prepared as follows: the medium was removed from the rapidly-growing semi-confluent PK-15 cells it was infected with the Kaplan strain of PRV (a multiplicity of infection of 0.1 plaque-forming unit/cell)
Summary
Pseudorabies virus (PRV) is a causative agent of Aujeszky’s disease (AD)[1] in pigs. PRV has a doublestranded DNA genome with a size of approximately 143 kbp. The Real-Time Sequencer II (RSII) and the Sequel 3rdGS platforms from Pacific Biosciences (PacBio) and the Oxford Nanopore Technologies (ONT) MinION 3rdGS device were used to characterize the static[18,19] and dynamic[20] PRV transcriptome These sequencing techniques, with the library preparation methods [e.g. non-amplified SMRT method and amplified, Iso-seq protocol from the PacBio; full-length cDNA-sequencing, direct RNA-sequencing, and cDNA-sequencing on 5′Cap-selected samples from ONT, (Fig. 1,2)] used in these studies made it possible to identify several hundreds of novel transcript isoforms (including 3′- and 5′ UTR variants, and splice isoforms), as well as dozens of protein-coding and non-coding RNAs and numerous complex transcripts of PRV. We provide a detailed overview of the library preparation techniques and a description of the data (Table 3, Figs. 1 and 2)
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