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

Jason R Miller; Kari A Dilley; Derek M Harkins; Timothy B Stockwell; Reed S Shabman; Granger G Sutton

doi:10.12688/f1000research.13580.3

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

F1000Res. 2018 Jan 23:7:98. doi: 10.12688/f1000research.13580.3. eCollection 2018.

Authors

Jason R Miller^{1

2}, Kari A Dilley¹, Derek M Harkins¹, Timothy B Stockwell^{1

3}, Reed S Shabman^{1

4}, Granger G Sutton¹

Affiliations

¹ J. Craig Venter Institute, Rockville, MD, 20850, USA.
² Shepherd University, Shepherdstown, WV, 25443, USA.
³ National Biodefense Analysis and Countermeasures Center (NBACC), Fort Detrick, MD, 21702, USA.
⁴ American Type Culture Collection, Gaithersburg, MD, 20877, USA.

Abstract

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.

Keywords: HepG2; HuH-7; Jurkat; RNAseq; host subtraction; human cell lines.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Line
DNA Viruses
Databases, Genetic*
High-Throughput Nucleotide Sequencing
Humans
Viruses

Grants and funding

JCVI staff was supported by DHS contract HSHQDC-15-C-B0059.