Data Descriptor: Transcriptome- wide survey of pseudorabies virus using next- and third-generation sequencing platforms Dóra Tombácz 1 , Donald Sharon 2 , Attila Szűcs 1 , Norbert Moldován 1 , Michael Snyder 2 & Zsolt Boldogkői 1 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. Design Type(s) transcription profiling by high throughput sequencing design • parallel group design Measurement Type(s) messenger RNA • total RNA • Coding Region Technology Type(s) RNA sequencing Factor Type(s) temporal_interval • assay material selection • cap analysis of gene expression • enzymatic amplification • size fractionation • nucleic acid library construction protocol • Technology Platform Sample Characteristic(s) Suid herpesvirus 1 strain Kaplan 1 Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary. 2 Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA. Correspondence and requests for materials should be addressed to Z.B. (email: boldogkoi.zsolt@med.u-szeged.hu). OPEN Received: 30 January 2018 Accepted: 28 March 2018 Published: 19 June 2018 www.nature.com/scientificdata SCIENTIFIC DATA | 5:180119 | DOI: 10.1038/sdata.2018.119 1