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A host subtraction database for virus discovery in human cell line sequencing data
- Source :
- F1000Research
- Publication Year :
- 2019
- Publisher :
- F1000 Research Limited, 2019.
-
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.
- Subjects :
- 0301 basic medicine
HepG2
viruses
Sequencing data
Human cell line
computer.software_genre
Jurkat cells
Virus
General Biochemistry, Genetics and Molecular Biology
Cell Line
03 medical and health sciences
0302 clinical medicine
Databases, Genetic
Humans
General Pharmacology, Toxicology and Pharmaceutics
030304 developmental biology
0303 health sciences
biology
Database
General Immunology and Microbiology
Host (biology)
Jurkat
Subtraction
HuH-7
RNA
High-Throughput Nucleotide Sequencing
General Medicine
Articles
Method Article
host subtraction
biology.organism_classification
RNAseq
Sendai virus
030104 developmental biology
Viruses
human cell lines
computer
030217 neurology & neurosurgery
Subjects
Details
- Language :
- English
- ISSN :
- 20461402
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- F1000Research
- Accession number :
- edsair.doi.dedup.....6088fd67572f0a0bf6c4a77eaa828362