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| Status |
Public on Jun 10, 2014 |
| Title |
Comparative total RNA and mRNA sequencing and systems analysis reveals nascent transcriptional response to early HIV-1 infection in a CD4+ T cell line |
| Organisms |
Homo sapiens; Human immunodeficiency virus 1 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To systematically investigate early host transcriptional response to HIV-1 infection, including polyadenylated and non-polyadenylated transcripts, we separately sequenced Total RNAs (Total RNA-seq) from HIV-1-infected SupT1 cells, a human CD4+ T cell line. We show many non-polyadenylated RNAs were also differentially expressed upon HIV-1 infection, as expected only detected by Total RNA-seq. Interestingly, we identified 8 times more differentially expressed genes at 12 hour post-infection by Total RNA-seq than by mRNA-seq, mostly protein-coding genes.
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| Overall design |
6 Total RNA sample sets were sequenced. Samples were either Mock infected, HIV-1 infected, or UV-inactivated viron infected for either 12 hours or 24 hours. Each sample set contains replicates.
mRNA-seq data was processed previously and is part of a different study. It was referenced in this study. The mRNA-seq data can be found in GSE38006. This data set refers to the Whole Transcriptome data from similar samples.
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| Contributor(s) |
Peng X, Sova P, Weiss J, Law GL, Palermo R, Katze MG |
| Citation(s) |
24850744 |
| |
| Submission date |
Jan 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
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| Organization name |
University of Washington
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| Department |
Microbiology
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| Lab |
Michael G. Katze, Ph.D
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| Street address |
Rosen Building 960 Republican St.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18160 |
Illumina HiSeq 2000 (Homo sapiens; Human immunodeficiency virus 1) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA234297 |
| SRA |
SRP035316 |
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