Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE144332
Status 2020/6/15
Title A unique viral reservoir landscape associated with durable natural control of HIV-1 infection [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected persons (“elite controllers”, ECs), despite the presence of a replication-competent viral reservoir. Such an ability to spontaneously maintain undetectable plasma viremia is a major objective of functional cure efforts, yet the characteristics of proviral reservoirs in ECs remain to be determined. Using single-genome, near full-length next-generation sequencing and chromosomal integration site analysis, we here show that proviral reservoirs of ECs frequently consist of oligoclonal to near monoclonal clusters of identical intact proviral sequences. In contrast to persons treated with long-term antiretroviral therapy, intact proviral species from ECs displayed highly distinct chromosomal integration sites in the human genome and were preferentially located in centromeric satellite DNA or in KRAB-ZNF genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, integration sites of intact proviruses from ECs showed increased distance to host transcriptional start sites and accessible chromatin and were enriched for repressive chromatin marks. These data suggest that a distinct proviral reservoir configuration represents a structural correlate of natural viral control, and that quality rather than quantity of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, failure to detect intact proviral sequences despite analyzing > 1.5 billion peripheral blood mononuclear cells in one EC raises the possibility that a sterilizing cure of HIV-1 infection, previously only observed following allogeneic hematopoietic stem cell transplantation, may be feasible in rare instances.
Samples
GSM ID Sample info Characteristics Description
GSM4286082 ART Patient 01 RNAseq Central memory CD4 T cells patient:ART Patient 01; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-ART-001
GSM4286083 ART Patient 01 RNAseq Effector memory CD4 T cells patient:ART Patient 01; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-ART-02
GSM4286084 ART Patient 01 RNAseq Naive CD4 T cells patient:ART Patient 01; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-ART-03
GSM4286085 ART Patient 01 RNAseq TEMRA CD4 T cells patient:ART Patient 01; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-ART-04
GSM4286086 ART Patient 01 RNAseq Total CD4 T cells patient:ART Patient 01; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-ART-05
GSM4286087 ART Patient 02 RNAseq Central memory CD4 T cells patient:ART Patient 02; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-ART-06
GSM4286088 ART Patient 02 RNAseq Effector memory CD4 T cells patient:ART Patient 02; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-ART-07
GSM4286089 ART Patient 02 RNAseq Naive CD4 T cells patient:ART Patient 02; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-ART-08
GSM4286090 ART Patient 02 RNAseq TEMRA CD4 T cells patient:ART Patient 02; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-ART-09
GSM4286091 ART Patient 02 RNAseq Total CD4 T cells patient:ART Patient 02; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-ART-10
GSM4286092 ART Patient 03 RNAseq Central memory CD4 T cells patient:ART Patient 03; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-ART-11
GSM4286093 ART Patient 03 RNAseq Effector memory CD4 T cells patient:ART Patient 03; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-ART-12
GSM4286094 ART Patient 03 RNAseq Naive CD4 T cells patient:ART Patient 03; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-ART-13
GSM4286095 ART Patient 03 RNAseq TEMRA CD4 T cells patient:ART Patient 03; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-ART-14
GSM4286096 ART Patient 03 RNAseq Total CD4 T cells patient:ART Patient 03; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-ART-15
GSM4286097 EC Patient 01 RNAseq Central memory CD4 T cells patient:EC Patient 01; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-001
GSM4286117 EC Patient 05 RNAseq Central memory CD4 T cells patient:EC Patient 05; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-021
GSM4286098 EC Patient 01 RNAseq Effector memory CD4 T cells patient:EC Patient 01; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-002
GSM4286099 EC Patient 01 RNAseq Naive CD4 T cells patient:EC Patient 01; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-003
GSM4286100 EC Patient 01 RNAseq TEMRA CD4 T cells patient:EC Patient 01; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-004
GSM4286101 EC Patient 01 RNAseq Total CD4 T cells patient:EC Patient 01; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-005
GSM4286102 EC Patient 02 RNAseq Central memory CD4 T cells patient:EC Patient 02; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-006
GSM4286103 EC Patient 02 RNAseq Effector memory CD4 T cells patient:EC Patient 02; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-007
GSM4286118 EC Patient 05 RNAseq Effector memory CD4 T cells patient:EC Patient 05; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-022
GSM4286104 EC Patient 02 RNAseq Naive CD4 T cells patient:EC Patient 02; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-008
GSM4286119 EC Patient 05 RNAseq Naive CD4 T cells patient:EC Patient 05; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-023
GSM4286105 EC Patient 02 RNAseq TEMRA CD4 T cells patient:EC Patient 02; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-009
GSM4286120 EC Patient 05 RNAseq TEMRA CD4 T cells patient:EC Patient 05; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-024
GSM4286121 EC Patient 05 RNAseq Total CD4 T cells patient:EC Patient 05; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-025
GSM4286122 EC Patient 06 RNAseq Central memory CD4 T cells patient:EC Patient 06; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-026
GSM4286106 EC Patient 02 RNAseq Total CD4 T cells patient:EC Patient 02; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-010
GSM4286123 EC Patient 06 RNAseq Effector memory CD4 T cells patient:EC Patient 06; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-027
GSM4286107 EC Patient 03 RNAseq Central memory CD4 T cells patient:EC Patient 03; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-011
GSM4286124 EC Patient 06 RNAseq Naive CD4 T cells patient:EC Patient 06; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-028
GSM4286108 EC Patient 03 RNAseq Effector memory CD4 T cells patient:EC Patient 03; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-012
GSM4286125 EC Patient 06 RNAseq TEMRA CD4 T cells patient:EC Patient 06; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-029
GSM4286109 EC Patient 03 RNAseq Naive CD4 T cells patient:EC Patient 03; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-013
GSM4286126 EC Patient 06 RNAseq Total CD4 T cells patient:EC Patient 06; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-030
GSM4286110 EC Patient 03 RNAseq TEMRA CD4 T cells patient:EC Patient 03; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-014
GSM4286127 EC Patient 07 RNAseq Central memory CD4 T cells patient:EC Patient 07; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-031
GSM4286111 EC Patient 03 RNAseq Total CD4 T cells patient:EC Patient 03; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-015
GSM4286112 EC Patient 04 RNAseq Central memory CD4 T cells patient:EC Patient 04; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-016
GSM4286113 EC Patient 04 RNAseq Effector memory CD4 T cells patient:EC Patient 04; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-017
GSM4286114 EC Patient 04 RNAseq Naive CD4 T cells patient:EC Patient 04; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-018
GSM4286115 EC Patient 04 RNAseq TEMRA CD4 T cells patient:EC Patient 04; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-019
GSM4286116 EC Patient 04 RNAseq Total CD4 T cells patient:EC Patient 04; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-020
GSM4286128 EC Patient 07 RNAseq Effector memory CD4 T cells patient:EC Patient 07; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-032
GSM4286129 EC Patient 07 RNAseq Naive CD4 T cells patient:EC Patient 07; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-033
GSM4286130 EC Patient 07 RNAseq TEMRA CD4 T cells patient:EC Patient 07; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-034
GSM4286131 EC Patient 07 RNAseq Total CD4 T cells patient:EC Patient 07; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-035
GSM4286132 EC Patient 08 RNAseq Central memory CD4 T cells patient:EC Patient 08; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-036
GSM4286133 EC Patient 08 RNAseq Effector memory CD4 T cells patient:EC Patient 08; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-037
GSM4286134 EC Patient 08 RNAseq Naive CD4 T cells patient:EC Patient 08; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-038
GSM4286135 EC Patient 08 RNAseq TEMRA CD4 T cells patient:EC Patient 08; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-039
GSM4286136 EC Patient 08 RNAseq Total CD4 T cells patient:EC Patient 08; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-040
GSM4286137 EC Patient 09 RNAseq Central memory CD4 T cells patient:EC Patient 09; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-041
GSM4286138 EC Patient 09 RNAseq Effector memory CD4 T cells patient:EC Patient 09; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-042
GSM4286139 EC Patient 09 RNAseq Naive CD4 T cells patient:EC Patient 09; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-043
GSM4286140 EC Patient 09 RNAseq TEMRA CD4 T cells patient:EC Patient 09; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-044
GSM4286141 EC Patient 09 RNAseq Total CD4 T cells patient:EC Patient 09; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-045
GSM4286142 EC Patient 10 RNAseq Central memory CD4 T cells patient:EC Patient 10; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-046
GSM4286143 EC Patient 10 RNAseq Effector memory CD4 T cells patient:EC Patient 10; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-047
GSM4286144 EC Patient 10 RNAseq Naive CD4 T cells patient:EC Patient 10; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-048
GSM4286145 EC Patient 10 RNAseq TEMRA CD4 T cells patient:EC Patient 10; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-049
GSM4286146 EC Patient 10 RNAseq Total CD4 T cells patient:EC Patient 10; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-050
GSM4286147 EC Patient 11 RNAseq Central memory CD4 T cells patient:EC Patient 11; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-051
GSM4286148 EC Patient 11 RNAseq Effector memory CD4 T cells patient:EC Patient 11; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-052
GSM4286149 EC Patient 11 RNAseq Naive CD4 T cells patient:EC Patient 11; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-053
GSM4286150 EC Patient 11 RNAseq TEMRA CD4 T cells patient:EC Patient 11; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-054
GSM4286151 EC Patient 11 RNAseq Total CD4 T cells patient:EC Patient 11; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-055
GSM4286152 EC Patient 12 RNAseq Central memory CD4 T cells patient:EC Patient 12; tissue:peripheral blood; replicate:1; cell type:Central memory CD4 T cells CJ-EC-056
GSM4286153 EC Patient 12 RNAseq Effector memory CD4 T cells patient:EC Patient 12; tissue:peripheral blood; replicate:1; cell type:Effector memory CD4 T cells CJ-EC-057
GSM4286154 EC Patient 12 RNAseq Naive CD4 T cells patient:EC Patient 12; tissue:peripheral blood; replicate:1; cell type:Naive CD4 T cells CJ-EC-058
GSM4286155 EC Patient 12 RNAseq TEMRA CD4 T cells patient:EC Patient 12; tissue:peripheral blood; replicate:1; cell type:TEMRA CD4 T cells CJ-EC-059
GSM4286156 EC Patient 12 RNAseq Total CD4 T cells patient:EC Patient 12; tissue:peripheral blood; replicate:1; cell type:Total CD4 T cells CJ-EC-060
Platform GPL21697  : NextSeq 550 (Homo sapiens)
Literature 32848246  35026153  36596305  
Download Download xCell Data  Download Expression Analysis Data  
xCell Plot
* p<0.05 ** p<0.01