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Series GSE80212 Query DataSets for GSE80212
Status Public on Dec 23, 2017
Title A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers (scRNA-Seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-Seq to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. We discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. We identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells (PBMCs) from healthy individuals in vitro.
 
Overall design Single-cell RNA-seq profiling of HIV-1-exposed cDCs and media controls from 3 elite controllers used to identify reproducible gene expression programs associated with cell-intrinsic HIV-1 immune recognition.
 
Contributor(s) Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG
Citation(s) 29378643
Submission date Apr 12, 2016
Last update date Mar 22, 2019
Contact name Michael B Cole
E-mail mbcole@berkeley.edu
Organization name UC Berkeley
Street address 378 Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (393)
GSM2898321 HIV_s1
GSM2898322 MED_s2
GSM2898323 HIV_s3
This SubSeries is part of SuperSeries:
GSE108445 A Reproducibility-Based Computational Framework Identifies An Inducible, Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers
Relations
BioProject PRJNA318284
SRA SRP073208

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

Supplementary file Size Download File type/resource
GSE80212_norm_log_tpm.csv.gz 8.4 Mb (ftp)(http) CSV
Raw data are available in SRA
Processed data is available on Series record
Processed data are available on Series record

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