A host subtraction database for virus discovery in human cell line sequencing data

The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected...

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Autores principales: Miller, Jason R., Dilley, Kari A., Harkins, Derek M., Stockwell, Timothy B., Shabman, Reed S., Sutton, Granger G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Method Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556987/
https://www.ncbi.nlm.nih.gov/pubmed/31231504
http://dx.doi.org/10.12688/f1000research.13580.3
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author Miller, Jason R.
Dilley, Kari A.
Harkins, Derek M.
Stockwell, Timothy B.
Shabman, Reed S.
Sutton, Granger G.
author_facet Miller, Jason R.
Dilley, Kari A.
Harkins, Derek M.
Stockwell, Timothy B.
Shabman, Reed S.
Sutton, Granger G.
author_sort Miller, Jason R.
collection PubMed
description The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.
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spelling pubmed-65569872019-06-20 A host subtraction database for virus discovery in human cell line sequencing data Miller, Jason R. Dilley, Kari A. Harkins, Derek M. Stockwell, Timothy B. Shabman, Reed S. Sutton, Granger G. F1000Res Method Article The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses. F1000 Research Limited 2019-05-21 /pmc/articles/PMC6556987/ /pubmed/31231504 http://dx.doi.org/10.12688/f1000research.13580.3 Text en Copyright: © 2019 Miller JR et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method Article
Miller, Jason R.
Dilley, Kari A.
Harkins, Derek M.
Stockwell, Timothy B.
Shabman, Reed S.
Sutton, Granger G.
A host subtraction database for virus discovery in human cell line sequencing data
title A host subtraction database for virus discovery in human cell line sequencing data
title_full A host subtraction database for virus discovery in human cell line sequencing data
title_fullStr A host subtraction database for virus discovery in human cell line sequencing data
title_full_unstemmed A host subtraction database for virus discovery in human cell line sequencing data
title_short A host subtraction database for virus discovery in human cell line sequencing data
title_sort host subtraction database for virus discovery in human cell line sequencing data
topic Method Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556987/
https://www.ncbi.nlm.nih.gov/pubmed/31231504
http://dx.doi.org/10.12688/f1000research.13580.3
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