GEO DataSets

(Submitter supplied) High levels of HIV-1 replication during the chronic phase of infection are usually associated with rapid disease progression (RP). However, a minority of HIV-infected individuals remain asymptomatic and show persistently high CD4+ T cell counts despite high viremia for many years (viremic non progressors, VNP). The latter profile is reminiscent of the non-pathogenic model of SIV infection in natural hosts such as the sooty mangabey. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

79 Samples

Download data: TXT

(Submitter supplied) In contrast to pathogenic HIV and SIV infection of humans and macaques, SIV infection of sooty mangabeys (SMs) is typically non-pathogenic despite high virus replication. A key feature of primary SIV infection of SMs is a strong type I interferon (IFN-I) response, characterized by massive up-regulation of interferon-stimulated genes (ISG), followed by rapid resolution during the acute-to-chronic phase transition and establishment of an immune quiescent state that persists throughout the chronic infection. more...

Organism:

Macaca mulatta; Cercocebus atys

Type:

Expression profiling by array

Dataset:

GDS4237

Platform:

GPL3535

47 Samples

Download data: CEL

Temporal analysis of whole blood from 8 naturally SIV-infected SMs treated with recombinant RM IFNalpha2-IgFc (rmIFNα2) for 16 weeks. SIV infection of SMs is typically non-pathogenic. Results provide insight into effects of experimentally-augmented IFN-I signaling in chronically SIV-infected SMs.

Organism:

Cercocebus atys; Macaca mulatta

Type:

Expression profiling by array, transformed count, 2 agent, 8 individual, 6 time sets

Platform:

GPL3535

Series:

GSE35460

47 Samples

Download data: CEL

(Submitter supplied) Pathogenic HIV/SIV infection of humans and rhesus macaques (RMs) induces persistently high production of type-I interferon (IFN-I) which is thought to contribute to disease progression. To elucidate the specific role of IFN in SIV pathogenesis, 12 RMs were treated prior to i.v. SIVmac239 infection with a high or a low dose of an antibody (AGS-009) that neutralizes most IFN subtypes, and compared with six mock-infused, SIV-infected controls. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

107 Samples

Download data: TXT

(Submitter supplied) Transcriptional Profiling Reveals Distinguishing Features of Immune Activation in the Lymphatic Tissues of Sooty Mangabeys and Rhesus Macaques in Early SIV Infection Immune activation in the chronic stages of HIV-1 and SIV infection of rhesus macaques is thought to play a critical role in CD4+ T cell depletion and progression to AIDS. Conversely, the lack of immune activation in the chronic stages of SIV infection of sooty mangabeys is thought to protect this species from a pathogenic outcome. more...

Organism:

Macaca mulatta; Cercocebus atys

Type:

Expression profiling by array

Dataset:

GDS4223

Platform:

GPL3535

28 Samples

Download data: CEL

(Submitter supplied) Natural SIV infection of sooty mangabeys (SMs) does not progress to disease despite chronic virus replication. In contrast to pathogenic SIV infection of rhesus macaques (RMs), chronic SIV infection of SMs is characterized by low immune activation. To elucidate the mechanisms underlying this phenotype, we longitudinally assessed host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs is consistently associated with a robust innate immune response, including widespread up-regulation of interferon-stimulated genes (ISGs). more...

Organism:

Macaca mulatta; Cercocebus atys

Type:

Expression profiling by array

Platform:

GPL3535

94 Samples

Download data: CEL

Temporal analysis of lymph nodes of SIVsmm infected Sooty mangabeys (SM) and SIVmac239 infected Rhesus macaques (RM). SIVsmm is non-pathogenic to host SM but origin of pathogens (HIV-2/SIVmac) to humans and RM. Results provide insight into the molecular basis of the differences in host responses.

Organism:

Cercocebus atys; Macaca mulatta

Type:

Expression profiling by array, count, 3 disease state, 3 infection, 2 species, 3 time sets

Platform:

GPL3535

Series:

GSE17626

28 Samples

Download data: CEL

(Submitter supplied) To characterize more broadly the effect of attenuated TLR4 signaling responses in sooty mangabeys, we performed a comparative RNA-seq profiling of LPS-treated primary monocytes from rhesus macaques and sooty mangabeys. Production of TNF- and IL6 mRNA was significantly lower in sooty mangabeys. Moreover, we observed that induction of NF-κB -regulated inflammatory genes was broadly and significantly reduced in sooty mangabeys, for TNF-a and IL-6 signaling pathways, compared to rhesus macaques. more...

Organism:

Macaca mulatta; Cercocebus atys

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23804 GPL23805

24 Samples

Download data: TXT

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca nemestrina; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27943 GPL33261

116 Samples

Download data: TXT

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:

Macaca nemestrina; Macaca mulatta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL33261 GPL27943

120 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Objective: To evaluate the effect of short-term type I IFN treatment on the latent viral reservoir in SIV-infected rhesus macaques on ART; Methods: We infected twelve RMs intrarectally with 10,000 TCID of SIVmac239. After 6 weeks of infection, all RMs started a three-class, four-drug ART regimen. Once viral loads were consistently undetectable, six animals were administered 1 dose of pegylated IFN-α2a per week for 4 weeks with each weekly intramuscular application being 6 µg/kg.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23804

35 Samples

Download data: TXT

(Submitter supplied) We examined the gene expression profiles in ex vivo human CD4+ and CD8+ T cells from untreated HIV-infected individuals at different clinical stages and rates of disease progression. Profiles of pure CD4+ and CD8+ T cells subsets from HIV-infected nonprogressors who controlled viremia were indistinguishable from HIV-uninfected individuals. Similarly, no gene clusters could distinguish T cells from individuals with early from chronic progressive HIV infection, whereas differences were observed between uninfected or nonprogressors versus early or chronic progressors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2649

Platform:

GPL96

40 Samples

Download data: CEL

Analysis of CD4+ and CD8+ T cells from HIV patients at different clinical stages and rates of disease progression. Changes in T-cell function are a hallmark of HIV infection. Results provide insight into the pathogenic mechanisms in HIV infections that lead to these changes in T-cell function.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 cell type, 4 disease state sets

Platform:

GPL96

Series:

GSE6740

40 Samples

Download data: CEL

(Submitter supplied) The molecular mechanisms underlying HIV-induced inflammation remain incompletely defined although they associate with morbidity and progression to AIDS. Here we used non-human primate models of pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infection in respectively macaques and African green monkeys. We longitudinally analyzed DNA methylation changes in CD4+ T cells from lymph node and blood using species-compatible probes on human 450K methylation BeadArrays. more...

Organism:

Homo sapiens; Chlorocebus sabaeus; Macaca mulatta

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

77 Samples

Download data: CSV, IDAT

(Submitter supplied) We assessed correlates of protection from disease progression in a rare subset of HIV-infected individuals, viremic non-progressors (VNPs). These individuals have high viral load for several years, but in contrast to the majority of infected individuals, they do not progress to AIDS. Here we found this lack of progression was associated with selective preservation of two essential subsets of memory CD4+ T cells, central memory (TCM) and stem-cell memory (TSCM) cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) In this study three Indian rhesus macaques were infected with Simian Immunodeficiency Virus (SIVmac251). This generates a chronic infection mirroring AIDS in the animals. Prior to infection (day 0) and at two different time-points post-infection (day 21 and day 90), intestinal resection biopsies were performed. The intestinal tissue was then separated into different sub-sections including lamina-propria lymphocytes (LPL), intra-epithelial lymphocytes (IEL), stroma or matrix and epithelium. more...

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

9 Samples

Download data: CEL, CHP