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.
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 |