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Series GSE111727 Query DataSets for GSE111727
Status Public on Mar 13, 2018
Title Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-infected Cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle towards HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression. We further validated our results using primary CD4+ T cells isolated from HIV+ individuals.
 
Overall design Human primary CD4+ T-cells were infected, cultured, and maintained in a resting, latent phenotype in order to generate a primary model of HIV latency. Latently infected cells were either left untreated, or exposed to SAHA or TCR stimulation, followed by single-cell isolation and single-cell RNA-seq (scRNA-Seq) analysis. Bulk RNA-Seq experiments were also performed as control. To validate the observed cellular heterogeneity in the primary model of HIV latency, we used primary CD4+ T cells isolated from HIV+ individuals. As for the primary HIV latency model, resting cells from HIV+ individuals were either not treated or TCR-treated before single cell isolation and single-cell RNA-Seq.
 
Contributor(s) Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A
Citation(s) 29694901
Submission date Mar 12, 2018
Last update date Mar 27, 2019
Contact name Monica Golumbeanu
E-mail(s) monica.golumbeanu@bsse.ethz.ch
Organization name ETH Z├╝rich
Department D-BSSE
Street address Mattenstrasse 26
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (387)
GSM3038071 Latency_model_untreated_cell_1
GSM3038072 Latency_model_untreated_cell_2
GSM3038073 Latency_model_untreated_cell_3
Relations
BioProject PRJNA437966
SRA SRP134967

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE111727_bulk_lat_model_raw_counts_genes.txt.gz 340.8 Kb (ftp)(http) TXT
GSE111727_sc_donors_normalized_counts_genes.txt.gz 2.1 Mb (ftp)(http) TXT
GSE111727_sc_donors_raw_counts_genes.txt.gz 890.0 Kb (ftp)(http) TXT
GSE111727_sc_lat_model_normalized_counts_genes.txt.gz 5.9 Mb (ftp)(http) TXT
GSE111727_sc_lat_model_raw_counts_genes.txt.gz 1.9 Mb (ftp)(http) TXT
GSE111727_sc_lat_model_raw_counts_spikes.txt.gz 7.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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