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| Status |
Public on May 16, 2012 |
| Title |
Next-generation sequencing reveals HIV-1-mediated suppression of T cell activation and RNA processing and the regulation of non-coding RNA expression in a CD4+ T cell line |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We sequenced the total mRNA from infected cells and detected differences in the expression of both host mRNA. We detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi providing new possible markers of virus-induced T cell cytopathology. By 24 hpi the expression of over 50% of detectable host loci was also altered indicating widespread alteration of host processes including RNA processing, splicing, and transport to an extent not previously reported. In addition next-generation sequencing provided insights into the expression of non-coding RNAs including microRNA host genes.
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| Overall design |
We isolated polyadenylated RNA from SUPT1 cells infected with HIV-1 strain LAI at 12 and 24 hours post-infection (3 replicates for each time point). As controls we isolated polyadenylated RNA from mock-infected cells at 12 and 24 hours post-infection (2 replicates at 12 hours post-infection, 3 replicates at 24 hours post-infection).
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| |
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| Contributor(s) |
Chang ST, Sova P, Peng X, Weiss J, Law GL, Palermo R, Katze MG |
| Citation(s) |
21933919 |
| Submission date |
May 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Michael G. Katze, Ph.D
|
| Street address |
Rosen Building 960 Republican St.
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA167037 |
| SRA |
SRP013224 |
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