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| Status |
Public on Feb 02, 2016 |
| Title |
Time course RNA-Seq of Innate Lymphoid Cells in Early Acute HIV Infection |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We apply RNA-seq to limited populations of Innate Lymphoid Cells type 2 and type 3 (ILC2s and ILC3s, respectively) in human individuals infected with acute HIV in the FRESH study. We measured the whole transcriptome of ILC2s and ILC3s in both untreated (n=2) and ART treated (n=2) individuals over the course of infection, in order to compare these populations at key points during infection, namely: viral detection, peak viremia, and weeks past peak viremia (6-7 weeks post detection). Lacking true biological replicates, HIV- patients in the same study (n=9) were used as replicates to conduct Differential Expression (DE) analysis between time points in both ILC2s and ILC3s on a patient by patient basis. In untreated patients, ILC2s and ILC3s differentially expressed genes associated with apoptosis and cell death between peak viremia and viral detection, while ART treated patients' ILC2s and ILC3s demonstrated a mitigated response. Comparing 6-7 weeks after detection with peak viremia revealed a relative decrease in genes associated in cell death in untreated patients, while ART treated patients showed varied responses where several DE genes were associated with immune response.
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| Overall design |
RNA-seq of two Innate Lymphoid Cell populations in 2 HIV+ untreated patients, 2 HIV+ ART treated patients, and 9 HIV- patients (control, replicates).
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| Contributor(s) |
Kloverpris HN, Kazer SW, Shalek AK, Walker BD, Ndung'u T, Leslie A |
| Citation(s) |
26850658 |
| Submission date |
Jan 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alasdair Leslie |
| E-mail(s) |
al.leslie@ahri.org
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| Organization name |
African Health Research Institute
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| Lab |
Leslie Lab
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| Street address |
719 Umbilo Road
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| City |
Durban |
| ZIP/Postal code |
4001 |
| Country |
South Africa |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA309415 |
| SRA |
SRP068722 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77088_ILCs_edgeR_processed_matrix.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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