ArticleGigaScience2018
Dynamic transcriptome profiling dataset of vaccinia virus obtained from long-read sequencing techniques.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Long-read transcriptomics of caviid gammaherpesvirus 1: compiling a comprehensive RNA atlas.mSystems · 2025Article
- Elucidating the Mechanism of VVTT Infection Through Machine Learning and Transcriptome Analysis.International journal of molecular sciences · 2025Article
- Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas.bioRxiv : the preprint server for biology · 2024Article
- Vaccinia virus Tiantan strain blocks host antiviral innate immunity and programmed cell death by disrupting gene expression.Biosafety and health · 2024Article
- Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches.mSphere · 2024Article
- In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing.Scientific data · 2023Article
- In-Depth Temporal Transcriptome Profiling of an Alphaherpesvirus Using Nanopore Sequencing.Viruses · 2022Article
- Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides.Scientific reports · 2021Article
- MinION nanopore sequencing and assembly of a complete human papillomavirus genome.Journal of virological methods · 2021Article
- Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay.Pathogens (Basel, Switzerland) · 2021Article
- Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome.Scientific reports · 2021Article
- Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.Scientific reports · 2021Article
- Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach.BMC research notes · 2021Article
- Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus.Viruses · 2021Article
- Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach.Frontiers in genetics · 2021Article
- Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing.Scientific reports · 2020Article
- Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection.Retrovirology · 2020Article
- Using Direct RNA Nanopore Sequencing to Deconvolute Viral Transcriptomes.Current protocols in microbiology · 2020Article
- Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background: Poxviruses are large DNA viruses that infect humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; however, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems and also allow direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date. Findings: For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods using the MinION device from Oxford Nanopore Technologies. Conclusions: By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions, and RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be used to analyze the currently available LRS platforms, library preparation methods, and bioinformatics pipelines.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.