Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA profile of THP-1 macrophage infected with different MTB strains

ABSTRACT: We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of (1) Beijing/W and non-Beijing/W clinical strains, and (2) susceptible and multidrug-resistant (MDR-) MTB strains. THP-1 cells were induced differentiation into a macrophage phenotype. Then cells were infected with three MDR (INHR, RIFR) Beijing/W, three sensitive (INHS, RIFS) Beijing/W, three MDR(INHR, RIFR) non-Beijing/W, and three sensitive (INHS, RIFS) non-Beijing/W strains. Total RNA were extracted and transfered into cDNA for miRNA profile analysis. Non-infected cells were used as control.

ORGANISM(S): Homo sapiens

SUBMITTER: Margaret Ip

PROVIDER: E-GEOD-65811 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

miRNA profile of THP-1 macrophage infected with different MTB strains

Project description:We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of (1) Beijing/W and non-Beijing/W clinical strains, and (2) susceptible and multidrug-resistant (MDR-) MTB strains.

2015-07-01 | GSE65811 | GEO

The global transcriptional profile of Mycobacterium tuberculosis during human macrophages infection

Project description:During lung infection Mycobacterium tuberculosis (Mtb) resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes. In this work we have analyzed by DNA microarray technique the global transcription profile of Mtb infecting primary human macrophages in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of Mtb. Keywords: time course We compared the global gene expression of the H37Rv strain of Mtb after 4 hours and 24 hours of infection of human macrophage-like THP-1 cells with the gene expression profile of the strain growing exponentially in broth cultures.

2010-05-27 | E-GEOD-6209 | biostudies-arrayexpress

Sigma factor E of Mycobacterium tuberculosis controls the expression of bacterial components that modulate macrophages

Project description:Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. In this work, we have identified the SigE regulon during infection of macrophages Our results indicate that SigE regulates the expression of genes involved in the maintenance of Mtb cell envelope integrity and function (i.e., detoxification and secretion). Keywords: strains comparison We compared the global gene expression of the H37Rv strain and the sigE mutant strain of Mtb in different conditions: growing exponentially in liquid media; after 2h of incubation in RPMI; or after 24 hours of infection of human macrophage-like THP-1 cells.

2010-05-25 | E-GEOD-7962 | biostudies-arrayexpress

Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I (SureQuant data)

Project description:CD8+ T cells contribute to protective immunity to Mycobacterium tuberculosis (Mtb), but the principles that govern presentation of Mtb peptides on MHC class I (MHC-I) on the surface of infected macrophages for CD8+ T cell recognition are incompletely understood. Here, we use internal standard parallel reaction monitoring (IS-PRM, also known as SureQuant) to rigorously validate identifications of Mtb-derived MHC-I peptides obtained in data-dependent MS analyses. We further use SureQuant to quantify presentation of Mtb peptides derived from the secreted effector proteins EsxA and EsxJ across multiple experimental conditions. We show that presentation of both EsxA- and EsxJ-derived peptides requires the activity of the mycobacterial ESX-1 type VII secretion system, possibly indicating that ESX-1-mediated phagosome membrane damage allows Mtb proteins to access MHC-I antigen processing pathways. We show that this requirement is independent of type I interferon signaling that occurs downstream of phagosome damage. Treatment with inhibitors of conventional proteolytic pathways involved in MHC-I antigen processing inhibits presentation of self peptides as expected, but does not inhibit presentation of Mtb peptides, implying an alternative or redundant mechanism of processing.

2023-04-24 | PXD037843 | Pride

Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 [whiB6_RNA-seq]

Project description:Among the multidrug-resistant (MDR) clones of Mycobacterium tuberculosis (Mtb) that were epidemiologically particularly successful, the 100-32 MDR Beijing clone, also called B0/W148 clone, has emerged since the early sixties. These B0/W148 strains belonging to the lineage 2 within the global Mtb phylogeny, are the main contributors to the MDR epidemic in Russia and Eastern Europe, and since the USSR’s fall, have also propagated to Western Europe. Among the various mutations that were identified as being specific for the MDR B0/W148 clone, we focused on two found in the transcriptional regulators KdpDE and WhiB6 and characterized in a H37Rv strain background the transcriptional profile associated with these mutations and their potential impact on the in vitro and in vivo growth characteristics.

2024-09-25 | GSE269918 | GEO

Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 [kdpDE_RNA-seq]

2024-09-25 | GSE269917 | GEO

Multifaceted dysfunction of infant airway macrophages in response to Mycobacterium tuberculosis

Project description:Infants are vulnerable to disseminated forms of tuberculosis and suffer disproportionately high morbidity and mortality, but the reasons for this are unknown. We hypothesized that since alveolar macrophages (AMs) are critical in the uptake and containment of Mycobacterium tuberculosis (Mtb) in the lung, their function may be impaired in early life. We developed a method of obtaining AMs during rigid bronchoscopy of healthy infants with suspected airway abnormality. RNAseq analysis of Mtb-stimulated AMs from 4 infants and 4 adults was performed.

2020-03-12 | E-MTAB-7679 | biostudies-arrayexpress

Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits

Project description:In our rabbit model of pulmonary tuberculosis, infection with Mtb HN878, a hyper-virulent W-Beijing strain, results in progressive cavitary disease. However, infection of rabbit lungs with Mtb CDC1551, a hyper-immunogenic strain is effectively controlled overtime, establishing latent Mtb infection. Using these two Mtb strains, we tested the hypothesis that the initial host response in the lungs within hours of infection determines later outcome. The microarray experiments was performed to identify gene expression changes in the Mtb-HN878 or CDC1551- infected rabbit lungs at 3 hours post infection, compared to uninfected naïve rabbit lungs. New Zealand White rabbits were infected with Mtb HN878 or CDC1551 at ~3.5log10. At 3 hours post infection, lung tissue from Mtb-infected and uninfected rabbits were isolated and used for total RNA extraction. Total rabbit lung RNA was used for microarray analysis to determine infection induced changes in host gene expression.

2013-08-17 | E-GEOD-49947 | biostudies-arrayexpress

Macrophage responses to MDR M.tuberculosis infection

Project description:The emergence of multidrug resistant (MDR) Mycobacterium tuberculosis (Mtb) strains, resistant to the frontline anti-tubercular drugs rifampicin and isoniazid, forces treatment with less effective and toxic second-line drugs and stands to derail TB control efforts. However, the immune response to MDR Mtb infection remains poorly understood. Here, we determined the RNA transcriptional profile of in vitro generated macrophages to infection with either drug susceptible Mtb HN878 or MDR Mtb W_7642 infection.

2018-12-26 | GSE115495 | GEO

Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I (DDA data)

Project description:Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a leading cause of infectious disease mortality worldwide for which no sufficiently protective vaccine exists. CD8+ T cells contribute to protective immunity to TB, but the antigenic targets presented on MHC-I by macrophages infected with virulent Mtb for recognition by CD8+ T cells have not been conclusively defined. Here, we use mass spectrometry to directly identify Mtb-derived peptides presented on MHC class I (MHC-I) by infected primary human monocyte-derived macrophages. We identified 16 MHC-I peptides derived from 12 Mtb proteins, and validated these identifications using internal standard parallel reaction monitoring (SureQuant). Our results show that this set of antigens is highly enriched for substrates of type VII secretion systems (T7SS) relative to the Mtb proteome. Our results identify specific Mtb proteins that may be suitable targets for subunit vaccines designed to elicit protective CD8+ T cell-mediated immunity and suggest that T7SS substrates may be a fruitful class of antigens to prioritize for further vaccine target discovery efforts. Note: donors labeled A, C, D, E, H, and I in file names here are renamed sequentially (A, B, C, D, E, and F) in the manuscript describing this study to avoid confusion.

2023-04-24 | PXD037837 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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