A host subtraction database for virus discovery in human cell

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. Jason R. Miller ( ) Corresponding author: [email protected] : Formal Analysis, Software, Writing – Original Draft Preparation; : Investigation; : Investigation; Author roles: Miller JR Dilley KA Harkins DM : Conceptualization, Investigation; : Conceptualization, Methodology, Supervision; : Formal Analysis, Stockwell TB Shabman RS Sutton GG Supervision No competing interests were disclosed. Competing interests: Miller JR, Dilley KA, Harkins DM How to cite this article: et al. A host subtraction database for virus discovery in human cell line 2018, :98 (doi: ) sequencing data [version 1; referees: awaiting peer review] F1000Research 7 10.12688/f1000research.13580.1 © 2018 Miller JR . This is an open access article distributed under the terms of the , which Copyright: et al Creative Commons Attribution Licence permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. JCVI staff was supported by DHS contract HSHQDC-15-C-B0059. Grant information: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. 23 Jan 2018, :98 (doi: ) First published: 7 10.12688/f1000research.13580.1 1,2 1 1 1,3