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| Status |
Public on Dec 31, 2018 |
| Title |
Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Throughout HIV-1 replication cycle, a complex interplay of host-pathogen interactions takes place in the infected cell, leading to production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while controlling intracellular defense. We have investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptome, proteome and phosphoproteome expression changes in infected and uninfected SupT1 CD4+ T cells at 5 time-points throughout the HIV-1 replication cycle. Genome-wide transcript levels were assessed by RNA-Seq, while protein and phosphoprotein relative abundances were obtained using SILAC mass spectrometry. By the means of a Gaussian mixed-effects model, we stratified host genes based on their gene expression temporal patterns at the three levels, showing how HIV may affect regulation of certain host genes. The results of the implemented integrative analysis of time-series omics data offers a catalogue of dynamic host response to HIV infection allowing a more comprehensive understanding of host-virus interactions. Furthermore, it facilitates identifying novel host factors potentially promoting or restricting HIV replication.
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| Overall design |
Host-HIV interactions in CD4+T-cells. Time-series RNA-Seq was performed in mock-treated and HIV-infected CD4+ T-cells at 6h, 12h, 18h, 24h and 30h.
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| Contributor(s) |
Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A |
| Citation(s) |
30659199 |
| Submission date |
Jun 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Monica Golumbeanu |
| E-mail(s) |
monica.golumbeanu@bsse.ethz.ch
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| Organization name |
ETH Zürich
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| Department |
D-BSSE
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| Street address |
Mattenstrasse 26
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA392230 |
| SRA |
SRP110659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100587_HIVeGFP_annotation.gtf.gz |
516 b |
(ftp)(http) |
GTF |
| GSE100587_HIVeGFP_sequence.fa.gz |
3.1 Kb |
(ftp)(http) |
FA |
| GSE100587_RNASeq_normalised_counts.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE100587_RNASeq_raw_counts.txt.gz |
603.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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