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Series GSE77088 Query DataSets for GSE77088
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
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.
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).
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
Organization name African Health Research Institute
Lab Leslie Lab
Street address 719 Umbilo Road
City Durban
ZIP/Postal code 4001
Country South Africa
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (40)
GSM2043730 110314 0450-318 ILC2
GSM2043731 110314 0450-318 ILC3
GSM2043732 180314 0450-318 ILC2
BioProject PRJNA309415
SRA SRP068722

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Supplementary file Size Download File type/resource
GSE77088_ILCs_edgeR_processed_matrix.txt.gz 1.4 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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