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Expression data from in vitro HIV-1-infected macrophages responding to phagocytic stimuli

ABSTRACT: We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 and then subjected to phagocytic stimuli; we identified distinct classes of differentially regulated genes during this process

ORGANISM(S): Homo sapiens

PROVIDER: GSE59991 | GEO | 2016/01/01

SECONDARY ACCESSION(S): PRJNA257220

REPOSITORIES: GEO

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Expression data from in vitro HIV-1-infected macrophages responding to phagocytic stimuli

Project description:We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 and then subjected to phagocytic stimuli; we identified distinct classes of differentially regulated genes during this process Primary human macrophages from 3 different donors were infected with HIV-1ADA WT or mock-infected for 8 days. They were incubated or not (basal) with IgG-SRBCs (FcR) or Salmonella Typhimurium (4/74 strain) during 1 hour at 37Â°C, then lysed and RNA of each sample was analyzed with microarrays.

2016-07-03 | E-GEOD-59991 | biostudies-arrayexpress

Expression data from in vitro HIV-1-infected macrophages responding to two SalmonellaTyphimurium bacteria

Project description:We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 or not and then subjected to contact with Salmonella Typhimurium ST313 or ST19 strains; we identified distinct classes of differentially regulated genes during this process

2024-07-09 | GSE116803 | GEO

Gene expression in phagocytic and non-phagocytic Entamoeba histolytica populations

Project description:The ability of Entamoeba histolytica to phagocytose host cells correlates to observed virulence in vivo. To better understand the mechanism of phagocytosis we used paramagnetic beads coated with host ligand and sorted trophozoites based on phagocytic ability. Gene expression was then measured in both the sorted phagocytic and non-phagocytic populations using a custom Affymetrix chip for E. histolytica. Feed forward regulation of phagocytosis by Entamoeba histolytica. Infection and Immunity. PMID 23045476 M280 Streptavidin Dynabeads (Invitrogen) were labeled with 20ug/mL biotinylated Human C1q (Quidel). Entamoeba histolytica (strain HM1) were washed twice with PBS then resuspended with the labeled beads at a 10:1 ratio of beads to trophozoites. Samples were incubated at 37Â°C for 45 minutes, washed twice with agitation to remove adherent beads, then resuspended in MACS buffer. Samples were loaded into magnetic columns (Miltenyi Biotec) and trophozoites were seperated according to manufacturer's protocols. phagocytic vs. non-phagocytic Entamoeba histolytica populations

2012-10-16 | E-GEOD-41604 | biostudies-arrayexpress

Expression data from different levels of ANA in HIV+ people

Project description:Different focal adhesions, gap junction, adherens junction, and tight junction, TLR signaling pathway were seen when compared the HIV+ high ANA (anti-nuclear antibodies) group with low ANA group We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

2018-10-01 | GSE101589 | GEO

Transcriptional characterization of phagocytic vs. non-phagocytic cells during Staphylococcus aureus craniotomy infection

Project description:scRNA-seq of phagocytic vs. non phagocytic immune cells during acute S. aureus craniotomy infection

2022-08-30 | GSE209622 | GEO

Gene expression in phagocytic and non-phagocytic Entamoeba histolytica populations

2012-10-16 | GSE41604 | GEO

Transcriptomic responses of human monocyte-derived dendritic cells to HIV and other innate stimuli

Project description:Transcriptomic responses of human monocyte-derived dendritic cells to HIV and other innate stimuli

| PRJNA517651 | ENA

Transcriptomic responses of human monocyte-derived dendritic cells to HIV and other innate stimuli

Project description:Transcriptional programming of the innate immune response is pivotal for host protection. The transcriptional mechanisms that link pathogen sensing with innate activation remain poorly understood. During infection with HIV-1, human dendritic cells (DCs) can detect the virus through an innate sensing pathway leading to antiviral type I interferon and DC maturation. Here, we have developed an iterative experimental and computational approach to map the innate response circuitry during HIV-1 infection. By integrating genome-wide chromatin accessibility with expression kinetics, we have inferred a gene regulatory network that links 542 transcription factors (TFs) with 21,862 target genes. Through genetic perturbation and drug treatments we identify PRDM1 and RARA as essential regulators of the interferon response and DC maturation, respectively. This work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting the complexity and cooperativity in the regulatory circuit controlling the DC response to HIV-1 infection.

2020-01-24 | GSE125817 | GEO

In vivo and in vitro proteome analysis of HIV-1 infected, human CD4+ T cells

Project description:Host directed therapies against HIV-1 are thought to be critical for long term containment of the HIV-1 pandemic but remain elusive. Since HIV-1 infects and manipulates important effectors of both the innate and adaptive immune system, identifying modulations of the host cell systems in humans during HIV-1 infection may be crucial for the development of immune based therapies. Here, we quantified the changes of the proteome in human CD4+ T cells upon HIV-1 infection, both in vitro and in vivo. A SWATH-MS approach was used to measure the proteome of human primary CD4+ T cells infected with HIV-1 in vitro as well as CD4+ T cells from HIV-1 infected patients with paired samples on and off antiretroviral treatment. In the in vitro experiment, the proteome of CD4+ T cells was quantified over a time course following HIV-1 infection. 1,725 host cell proteins and 4 HIV-1 proteins were quantified, with 145 proteins changing significantly during the time course. Changes in the proteome peaked 24 hours after infection, concomitantly with significant HIV-1 protein production. In the in vivo branch of the study, CD4+ T cells from viremic patients and those with no detectable viral load after treatment were sorted and the proteomes quantified. We consistently detected 895 proteins, 172 of which were considered to be significantly different between viraemic patients and patients undergoing successful treatment. The proteome of in vitro infected CD4+ T cells was modulated on multiple functional levels, including TLR-4 signalling and the type 1 interferon signalling pathway. Perturbations in the type 1 interferon signalling pathway were recapitulated in CD4+ T cells from patients. The study shows that proteome maps generated by SWATH-MS indicate a range of functionally significant changes in the proteome of HIV infected human CD4+ T cells. Exploring these perturbations in more detail may help identify new targets for immune based interventions.

2017-02-28 | PXD005234 | Pride

Expression data from primary human leukocytes (peropheral blood mononuclear cells, PBMC) cultured in vitro with HIV-1MN, HIV-2NIH-Z, CpG-A ODN or media alone

Project description:HIV-1 and HIV-2 can both infect humans, but HIV-2 causes a slow progressing disease and is well controlled by the immune system for prolonged period of times. Here we tested acute response aainst HIV-1 and HIV-2 exposure in peripheral blood mononuclear cells (PBMC) from three indepednent donors. A total of 24 samples were analyzed. PBMC from three donors were cultured with Media alone, HIV-1MN, HIV-2NIH-Z or the TLR9 agonist CpG-A (4 conditions), and cells were harvested at 6h and 12h (2time points) for RNA extraction.

2014-07-02 | E-GEOD-58994 | biostudies-arrayexpress

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