GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

171 Samples

Download data

(Submitter supplied) HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently considered ‘‘transcriptionally silent,’’ but active viral gene expression may occur in some cells, challenging the concept of viral latency. Applying an assay for profiling the transcriptional activity and the chromosomal locations of individual proviruses, we describe a global genomic and epigenetic map of transcriptionally active and silent proviral species and evaluate their longitudinal evolution in persons receiving suppressive ART. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

3 Samples

Download data: BED, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

75 Samples

Download data: CSV

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

96 Samples

Download data: BED

(Submitter supplied) Jurkat T cells (in triplicate per treatment group) were left untreated in culture, infected with VSV-G-pseudotyped HIV-based vector (which transduces Tat and eGFP) or treated with TNFalpha. Keywords: parallel sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1397

Platform:

GPL96

9 Samples

Download data

Analysis of Jurkat T cells infected with an HIV-based vector transducing green fluorescent protein. Expression of genes hosting HIV integration events examined. Results provide insight into how expression from the HIV type 1 promoter is affected by the integration site of the provirus.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 agent sets

Platform:

GPL96

Series:

GSE2504

9 Samples

Download data

(Submitter supplied) In this study, we determined the effect of proviral inducibility on CD8+ T cell recognition of HIV-infected clones. We showed that a T cell clone containing a provirus integrated in relatively transcriptionally inactive site was much less recognized by CD8+ T cells than a T cell clone containing a provirus that was integrated into a trancriptionally active site.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL32242

12 Samples

Download data: TXT

(Submitter supplied) Antiretroviral therapy controls but does not cure HIV-1 infection due to a reservoir of rare CD4 + T cells harboring latent proviruses. Little is known about the transcriptional program of latent cells. Here we report a novel strategy to enrich clones of latent cells carrying intact, replication-competent HIV-1 proviruses from blood based on their expression of unique T cell receptors. Latent cell enrichment enabled single cell transcriptomic analysis of 1,050 CD4 + T cells belonging to expanded clones harboring intact HIV-1 proviruses from 6 different individuals. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21697 GPL24676

18 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL30173

204 Samples

Download data: NARROWPEAK

(Submitter supplied) CD4 T cells with latent HIV-1 infection persist despite treatment with currently available antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may increase the immunological vulnerability of HIV-1-infected cells, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized, controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-a2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target site for panobinostat. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

153 Samples

Download data: NARROWPEAK

(Submitter supplied) CD4 T cells with latent HIV-1 infection persist despite treatment with currently available antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may increase the immunological vulnerability of HIV-1-infected cells, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized, controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-a2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target site for panobinostat. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

51 Samples

Download data: CSV

(Submitter supplied) Jurkat T-cells were latently infected with a defective HIV provirus carrying a GFP reporer gene. The cells were superinfected with a lentiviral vector expressing shRNA to NELF-E. The impact of NELF-depletion on RNAP II distribution on cellular genes and the HIV provirus was measured by ChIP-Seq. Data sets contained between 45 and 56 million mapped reads

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: BED, TXT, WIG

(Submitter supplied) HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here we determine HIV-1 integration sites (IS), associate them to chromatin and expression signatures at different genomic scales in a microglia cell model and profile them together with the primary T cell reservoir. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20795

2 Samples

Download data: CSV, FASTA

(Submitter supplied) We performed ChIP-seq in a microglia cell line (C20) upon CTCF-KD and CTCF-NT (wild-type) to understand the impact of CTCF loss on chromatin and HIV-1 integration pattern in the C20 cell line.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: BROADPEAK, BW, NARROWPEAK

(Submitter supplied) We performed RNA-seq in a microglia cell line (C20). Our aim was to understand how expression in the uninfected state will impact integration site selection on microglia.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: TAB

(Submitter supplied) We performed LM-PCR in an infected microglia cell line (C20) to map HIV-1 integration sites. Our aim was to compare the IS obtained through this method with ChIP-seq, ATAC-seq, and RNA-seq data obtained in the uninfected cells, allowing the assessment of integration preferences.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15520

14 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520 GPL24676

49 Samples

Download data: BED, BROADPEAK, BW, NARROWPEAK, TAB

(Submitter supplied) We performed ChIP-seq in a microglia cell line (C20) to understand integration patterns of HIV-1. We characterised the uninfected epigenetic cellular landscape in order to assess how integration is affected by distinct chromatin states and to understand the features defining integration-permissible regions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: BW

(Submitter supplied) We performed ATAC-seq in a microglia cell line (C20) to assess chromatin accessibility alterations upon HIV-1 infection in latent and active status in comparison with the uninfected status.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21697

4 Samples

Download data: BED, MTX, TXT