Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nef transfection of Jurkat T cells

ABSTRACT: Jurkat T cell line was transfected with SIV Nef controlled by an unducible promoter system. Nef was induced by addition of 10 micromolar pronasterone A and gene expression values were determined after 24 hrs. Control Jurkat cells were untransfected and treated with 10 micromolar pronasterone A and gene expressio values were determined after 24 hrs. Keywords: SIV Nef, Jurkat, pronasterone A

ORGANISM(S): Homo sapiens

PROVIDER: GSE4785 | GEO | 2006/07/25

SECONDARY ACCESSION(S): PRJNA95541

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Jurkat CF4+ T cells transfected with simian immunodeficiency virus Nef cells leads to a molecular profile of viral persistence and immune evasion.

Project description:Jurkat T cell line was transfected with SIV Nef controlled by an inducible promoter system. Nef was induced by addition of 10 micromolar pronasterone A and gene expression values were determined after 24 hrs. Control Jurkat cells were untransfected and treated with 10 micromolar pronasterone A and gene expressio values were determined after 24 hrs. Experiment Overall Design: Experimental conditions: 24 hr SIV Nef expression at physiological concentrations in T cells. Experiment Overall Design: Controls: Non-transfected. 24 hr.

2007-10-26 | E-GEOD-4785 | biostudies-arrayexpress

Gene expression in the blood of Live Attenuated Rev-Independent Nef¯SIV infected Rhesus macaques during acute infection

Project description:Rhesus macaques (RMs) inoculated with live-attenuated Rev-Independent Nef¯ simian immunodeficiency virus (Rev-Ind Nef¯SIV) as adults or neonates controlled viremia to undetectable levels and showed no signs of immunodeficiency over 6-8 years of follow-up. We tested the capacity of this live-attenuated virus to protect RMs against pathogenic, heterologous SIVsmE660 challenges

2013-08-09 | GSE49663 | GEO

Nef-mediated downmodulation of CD3 dampens immune activation and is critical for maintenance of high virus loads in SIV-infected macaques

Project description:The inability of Nef to downmodulate the T cell receptor CD3 distinguishes HIV-1 from most other primate lentiviruses and may contribute to its high virulence. However, the role of this Nef function in viral immune evasion and pathogenicity remained speculative. Here, we selectively disrupted this Nef activity in SIVmac239 and analyzed the consequences for the virological, immunological and clinical outcome of infection in rhesus macaques. The inability to downmodulate CD3 did not affect viral replication during acute infection but was associated with increased immune activation and antiviral gene expression. Thus, Nef-mediated downmodulation of CD3 dampens the inflammatory response to SIV infection and is critical for viral immune evasion.

2020-03-09 | GSE141626 | GEO

Gene expression profile in CD4+ T-cell infection with a SIV mutant related to altered humoral immune responses

Project description:A mutant simian immunodeficiency (SIVmac239) virus, found to be selected within chronically SIV-infected Burmese rhesus monkeys with relatively enhanced SIV-specific antibody responses, was reconstituted as a molecular clone. The virus (SIV Nef G63E) was then subjected to a preliminary analysis for their intracellular signal transduction and gene expression modulation patterns (as compared with wild type SIVmac239) within infected CD4+ T cells. Analysis implicated that the mutant virus had a moderately enhanced cytopathic phenotype. A SIV mutation (SIVmac239 Nef G63E) found to be enriched in rhesus monkeys with enhanced SIV-specific antibody responses was reconstituted on a pBR-based SIV molecular clone pBRmac239. HSC-F cynomolgus macaque central memory Th2-like T cells were infected with mutant and wild type SIVmac239 at MOI 5 in triplicate along with uninfected controls (i.e. a total of 9 samples) for 24 hours and subjected to analysis of their gene expression patterns.

2016-07-03 | E-GEOD-65806 | biostudies-arrayexpress

Expression data from rhesus macaque blood CD8+ T cells

Project description:Immunization of macaques with simian immunodeficiency virus with deletions in nef (SIV?nef) has been shown to elicit protective immunity to infection by pathogenic SIV, yet our understanding of the mechanisms that orchestrate protection and prevent pathogenesis remains limited. In the study, we utilize whole-genome transcriptional profiling to reveal molecular signatures of protective immunity in circulating CD8+ T cells of rhesus macaques vaccinated with SIVmac239?nef and challenged with pathogenic SIVmac251. Microarrays were used to characterize changes in gene expression in blood CD8+ T cells that occur following vaccination of rhesus macaques with attenuated SIV?nef and subsequent challenge with pathogenic SIVmac251, in comparison to corresponding changes in healthy controls and unvaccinated animals infected with pathogenic SIVmac251 CD8+ T cells were isolated by magnetic beads from the blood of healthy uninfected macaques, macaques vaccinated with SIV?nef, and unvaccinated controls infected with SIVmac251, and used for RNA extraction and hybridization on Affymetrix microarrays. Blood samples from vaccinated animals were collected prior to vaccination, at 3, 20, and 40 weeks following vaccination. After the 40 week vaccination period, macaques were challenged with SIVmac251, and blood was again collected at 3 weeks following challenge. Blood was collected from the unvaccinated controls at 3 weeks following infection with SIVmac251

2014-09-26 | E-GEOD-61766 | biostudies-arrayexpress

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [miRNA]

Project description:Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells Results: Differences in a set of microRNAs Conclusions: Nef-transfection induces changes in the microRNA content of exosomes

2018-11-18 | GSE122656 | GEO

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [mRNA]

Project description:Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells. Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells. Results: Differences in a set of mRNAs. Conclusions: Nef-transfection might induces changes in the mRNA content of exosomes.

2018-11-18 | GSE122655 | GEO

Multiple changes at the mucosal surface are induced by protective SIV vaccination

Project description:Systemic vaccination with the attenuated virus SIVmac239-∆Nef provides sterilizing or partial protection to rhesus monkeys challenged with WT SIV strains, providing important opportunities to study key immunological components of a protective host response. Here we show that intravenous vaccination with SIVmac239-∆Nef provides two potentially crucial immunological barriers localized at mucosal surfaces that correlate with the vaccine’s protective effects against WT SIVmac251 vaginal challenge: 1) a conditioned and coordinated response from the mucosal epithelium that blunts the early inflammatory and chemotactic signalling cascade that aids virus propagation and expansion; 2) early on-site generation/diversification of SIV-specific Abs from ectopic germinal center-like lymphoid aggregates. This unique host response to WT SIVmac251 in the female reproductive tract of SIVmac239-∆Nef-vaccinated animals points to a multi-layered strategy for a protective host response during immunodeficiency virus exposure—rapid induction of humroal immunity at mucosal surfaces without the deleterious inflammatory side effects tied to innate recognition of virus. This vaccine-induced host response highlights potential key protective mechanisms needed for an effective HIV vaccine Total RNA was isolated from the cervix of 17 Indian Rhesus macaques (3 uninfected animals; 5 unvaccinated animals 4-5 days post vaginal exposure with SIVmac251; 4 SIVmac239-∆Nef-vaccinated animals before challenge; 5 SIVmac239-∆Nef-vaccinated animals 4-5 days post vaginal exposure with SIVmac251) and prepared for hybridization on Affymetrix GeneChip Rhesus Macaque Genome Arrays. Replicate arrays were performed for a number of the samples to minimize assay noise and significant host genes altered during virus exposure in female reproductive tract tissue were identified by their associated q-values (< 0.2) and fold change in expression (> 1.2).

2012-05-30 | E-GEOD-33251 | biostudies-arrayexpress

Characterization of mammalian NEF-sp as a testis-specific nuclear 3′→5′ exoribonuclease

Project description:Ribonucleases catalyse maturation of functional RNAs or mediate degradation of cellular transcripts, activities that are critical for gene expression control. Here we identify a previously uncharacterized mammalian nuclease family member NEF-sp (LOC81691) as a testis-specific factor. Recombinant human NEF-sp demonstrates a divalent metal ion-dependent 3′→5′ exoribonuclease activity. This activity is specific to single-stranded RNA substrates and is independent of their length. Presence of a 2′-O-methyl modification at the 3′ end of the RNA substrate is inhibitory. Ectopically-expressed NEF-sp localizes to the nucleolar/nuclear compartment in human cell cultures and this is dependent on an N-terminal nuclear localization signal. Finally, mice lacking NEF-sp are viable and display normal fertility, likely indicating overlapping functions with other nucleases. Taken together, our study provides the first biochemical and genetic exploration of the role of the NEF-sp exoribonuclease in the mammalian genome.

2017-07-04 | GSE97235 | GEO

Gene expression profiling of CD4+ T cell line due to presence of Nef during HIV-1 infection.

Project description:We have utilized microarray technology to compare gene expression profile in presence or absence of Nef during HIV-1 infection in T cell-line. We found several genes significantly differentially regulated due to ∆nef HIV-1 infection and WT HIV-1 infection when compared to Uninfected cells and also several genes significantly dergulated due to WT HIV-1 infection as compared to ∆nef HIV-1 infection. We redistributed genes belonging to several gene ontology into broad categories like “signaling”, “apoptosis”, “transcription” and “lipid metabolism”. We selected some lipid metabolism genes to validate the Nef directed differential expression using quantitative real-time RT-PCR. Thus the present work highlights the importance of Nef directed differential gene expression in milieu of other viral proteins present during infection.

2016-12-06 | GSE76793 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data