ArticleJournal of virology2012
Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.
Article in Journal of virology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 29 citations in OpenAlex.
- Pathogenic Role of Epstein-Barr Virus in Lung Cancers.Viruses · 2021Review
- Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B).Scientific reports · 2020Article
- Murine xenograft bioreactors for human immunopeptidome discovery.Scientific reports · 2019Article
- Article
- Article
- From trash to treasure: detecting unexpected contamination in unmapped NGS data.BMC bioinformatics · 2019Article
- The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.BMC bioinformatics · 2019Article
- Global transcript structure resolution of high gene density genomes through multi-platform data integration.Nucleic acids research · 2016Article
- A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association.Acta neuropathologica communications · 2016Article
- Latent Expression of the Epstein-Barr Virus (EBV)-Encoded Major Histocompatibility Complex Class I TAP Inhibitor, BNLF2a, in EBV-Positive Gastric Carcinomas.Journal of virology · 2015Article
- Frequent infection of human cancer xenografts with murine endogenous retroviruses in vivo.Viruses · 2015Article
- A comprehensive transcriptional portrait of human cancer cell lines.Nature biotechnology · 2015Article
- High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project.Journal of virology · 2015Article
- Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples.PLoS pathogens · 2014Article
- Article
- Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.Journal of virology · 2014Article
- Targeting xCT, a cystine-glutamate transporter induces apoptosis and tumor regression for KSHV/HIV-associated lymphoma.Journal of hematology & oncology · 2014Article
- Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.Journal of virology · 2013Article
- Partial molecular cloning of the JHK retrovirus using gammaretrovirus consensus PCR primers.Future virology · 2013Article
- Limited RNA editing in exons of mouse liver and adipose.Genetics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Many cell lines commonly used for biological studies have been found to harbor exogenous agents such as the human tumor viruses Epstein-Barr virus (EBV) and human papillomavirus. Nevertheless, broad-based, unbiased approaches to globally assess the presence of ectopic organisms within cell model systems have not previously been available. We reasoned that high-throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell systems. Here we have used our RNA-seq analysis pipeline, PARSES (Pipeline for Analysis of RNA-Seq Exogenous Sequences), to investigate the presence of ectopic organisms within two EBV-positive B-cell lines commonly used by EBV researchers. Sequencing data sets from both the Akata and JY B-cell lines were found to contain reads for EBV, and the JY data set was found to also contain reads from the murine leukemia virus (MuLV). Further investigation revealed that MuLV transcription in JY cells is highly active. We also identified a number of MuLV alternative splicing events, and we uncovered evidence of APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G)-dependent DNA editing. Finally, reverse transcription-PCR analysis showed the presence of MuLV in three other human B-cell lines (DG75, Ramos, and P3HR1 Cl.13) commonly used by investigators in the Epstein-Barr virus field. We believe that a thorough examination of tissue culture microbiomes using RNA-seq/PARSES-like approaches is critical for the appropriate utilization of these systems in biological studies.
Indexed as
Identifiers
What OpenQuestion holds
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.