|
| Status |
Public on Feb 27, 2018 |
| Title |
Single cell transcriptional dynamics of flavivirus infection |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.
|
| |
|
| Overall design |
Dengue and Zika virus huh7 cells were subjected to virus-inclusive single cell RNA-Seq.
|
| |
|
| Contributor(s) |
Zanini F, Pu S, Bekerman E, Einav S, Quake SR |
| Citation(s) |
29451494 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U19 AI057229 |
Genomics Core |
STANFORD UNIVERSITY |
STEPHEN R QUAKE |
|
| |
| Submission date |
Feb 12, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Fabio Zanini |
| E-mail(s) |
fabio.zanini@fastmail.fm
|
| Organization name |
University of New South Wales
|
| Lab |
Zanini
|
| Street address |
High and Botany St
|
| City |
Kensington |
| State/province |
NSW |
| ZIP/Postal code |
2033 |
| Country |
Australia |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (2260)
|
|
| Relations |
| BioProject |
PRJNA433871 |
| SRA |
SRP132726 |
Less...
More...