Virus Expression Database

GSE40718

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis

Submitted by Ruth R Montgomery (Yale University School of Medicine, USA) on Sep 09 2012

Platform: ngs – Illumina Genome Analyzer II (Homo sapiens)

Pubmed: 23881275

Summary Background: West Nile virus is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV.

Results: From a total of 50 million reads per sample, we employed a Bayesian hierarchical mixture model to identify 4,026 transcripts that were differentially expressed after infection. Both predicted and novel gene changes were detected, as were gene isoforms, and while many of the genes were expressed by all donors, some were unique. Knock-down of genes not previously known to be associated with WNV resistance identified their critical role in control of viral infection.

Conclusions: Our study distinguishes both common gene pathways as well as novel cellular responses. Such analysis will be valuable for translational studies of susceptible and resistant individuals -- and for targeting therapeutics -- in multiple biological settings.

20 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM999654 Subject1 Mock macrophage  24 hrs mock Uninfected
GSM999655 Subject1 WNV macrophage  24 hrs WNV West Nile virus
GSM999656 Subject2 Mock macrophage  24 hrs mock Uninfected
GSM999657 Subject2 WNV macrophage  24 hrs WNV West Nile virus
GSM999658 Subject3 Mock macrophage  24 hrs mock Uninfected
GSM999659 Subject3 WNV macrophage  24 hrs WNV West Nile virus
GSM999660 Subject4 Mock macrophage  24 hrs mock Uninfected
GSM999661 Subject4 WNV macrophage  24 hrs WNV West Nile virus
GSM999662 Subject5 Mock macrophage  24 hrs mock Uninfected
GSM999663 Subject5 WNV macrophage  24 hrs WNV West Nile virus
GSM999664 Subject6 Mock macrophage  24 hrs mock Uninfected
GSM999665 Subject6 WNV macrophage  24 hrs WNV West Nile virus
GSM999666 Subject7 Mock macrophage  24 hrs mock Uninfected
GSM999667 Subject7 WNV macrophage  24 hrs WNV West Nile virus
GSM999668 Subject8 Mock macrophage  24 hrs mock Uninfected
GSM999669 Subject8 WNV macrophage  24 hrs WNV West Nile virus
GSM999670 Subject9 Mock macrophage  24 hrs mock Uninfected
GSM999671 Subject9 WNV macrophage  24 hrs WNV West Nile virus
GSM999672 Subject10 Mock macrophage  24 hrs mock Uninfected
GSM999673 Subject10 WNV macrophage  24 hrs WNV West Nile virus