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

Streptococcus pneumoniae cDNA microarray data used to characterize the transcriptional responses occurring during initial contact between pneumococci and a human pleural mesothelial cell line (PMC) in vitro.

ABSTRACT: Streptococcus pneumoniae (Spn) is a major causative organism of empyema, an inflammatory condition occurring in the pleural sac. In this study, we used Spn cDNA microarrays to characterize the transcriptional responses occurring during initial contact between Spn and a human pleural mesothelial cell line (PMC) in vitro

ORGANISM(S): Streptococcus pneumoniae

SUBMITTER: Anish Pandey

PROVIDER: E-MTAB-3931 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: Unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay

Project description:In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5' untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here, we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is a target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5'-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3'-end. Corresponding variations in protein levels led us to hypothesize that coordinated RNA decay represents another level in the hierarchical methionine biosynthesis control network to adjust methionine biosynthesis enzyme amounts to current metabolic requirements.

2021-02-18 | PXD022677 | Pride

Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: Unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay

2021-08-10 | PXD020619 | Pride

SNP search in NAD+ resistent Streptococcus pneumoniae

Project description:To gain deeper insights into antibacterial mechanisms of NAD+ and bacterial adaptation, we generated and sequenced NAD+ resistant clones of Spn. For this purpose, Spn was cultivated in liquid medium with increasing concentrations (50 µM to 5 mM) of NAD+. After six passages, bacteria were plated on blood agar supplemented with 500 µM NAD+ and three clones were picked

2023-06-11 | E-MTAB-12644 | biostudies-arrayexpress

Transcriptional response of monocyte-derived macrophages to stimulation with wildtype or pneumolysin-deficient Streptrococcus pneumoniae in the presence or absence of cytochalasin D

Project description:We used genome-wide transcriptional profiling by microarray to assess the contribution of pneumolysin on macrophage innate immune responses to the TIGR4 strain of Streptococcus pneumoniae (Spn). We focused on the early transcriptional responses at 4 hours after inoculation of human blood monocyte-derived macrophage cultures with Spn at a multiplicity of 10 bacteria to each cell. We compared transcriptomes in the presence and absence of wildtype or pneumolysin-deficient TIGR4 Spn, and also in the presence and absence of cytochalasin D to assess whether there is a differential effect of pneumolysin on innate immune responses with and without bacterial internalisation.

2021-03-31 | E-MTAB-8947 | biostudies-arrayexpress

Pathogenic Bacteria Exploit Transferrin Receptor Transcytosis to Penetrate the Blood‒Brain Barrier

Project description:In this study, we present evidence showing that the infection with the major meningitis-causing bacteria, NMEC, GBS and SPN, activates the same fusion process of bacteria-containing vesicles (BCVs) with TfR vesicles, which enables those bacteria to exploit TfR transcytosis to penetrate the BBB, and illustrate the details of this process in HBMECs and mouse models.

2023-10-24 | PXD039060 | Pride

Proteomic investigation into the action mechanism of inhibitor ptsc1 against Streptococcus pneumoniae

Project description:Phenyl-thiazolylurea-sulfonamides compound 1 (ptsc1) is a new and efficient bacterial inhibitor. Although the inhibitor has antibacterial activity against several model bacteria, the details of its mechanism in Streptococcus pneumoniae (S. pneumoniae) have not been revealed. In the current study, we found that ptsc1 can significantly inhibit the growth of S. pneumoniae. To further investigate the molecular mechanism of its antibacterial effects, quantitative proteomics was performed to identify differential expressed proteins in S. pneumoniae. Compared with the normal group, the expression levels of 38 proteins were upregulated, whereas those of 88 proteins were downregulated (> 1.3 fold-change) in the experimental group (P < 0.05). KEGG pathways analysis revealed that ptsc1 regulated proteins were mainly involved in carbohydrate metabolism, DNA replication and repair, pyrimidine metabolism, fatty acid biosynthesis and oxidative phosphorylation pathways. The results of GO enrichment analysis showed that the inhibitor could lead to dysregulation of bacterial translation and energy metabolism, and cause intracellular oxidative stress.

2022-01-12 | PXD030534 | Pride

RNA expression profiling in primary and immortalized human mesothelial cells, and in human vein and microvascular endothelial cells

Project description:Mesothelial cells, which interact with endothelial cells, are widely used in research including cancer and drug development, have not been comprehensively profiled. We therefore performed RNA sequencing of polarized, primary peritoneal (HPMC) and immortalized pleural mesothelial cells (MeT-5A), and compared it to endothelial cells from umbilical vein (HUVEC) and cardiac capillaries (HCMEC).

2023-05-24 | E-MTAB-12021 | biostudies-arrayexpress

Treatment of CHRF288-11 Megakaryocytic Cells with Wnt compounds

Project description:CHRF288-11 cells were treated with Wnt3a (150ng/ml) and/ot Wnt5a (1200ng/ml) and RNA was harvested after 8 hours of treatment Gene expression was analysed using Human WG6 V3 Illumina Beadarrays There are four experimental groups (Wnt3a Treated, Wnt5a Treated, Wnt3a + Wnt5a treated and Untreated (control)), each with three biological replicates

2012-11-07 | E-GEOD-42071 | biostudies-arrayexpress

Project description:SPN carriage

| PRJNA697931 | ENA

Changes in gene expression in fruitfly ovaries in mutants affecting components of rasiRNA system

Project description:rasiRNA (rasiRNAs, repeat-associated short interfering RNAs) system is a mechanism of silencing of mobile element transpositions in germline of a number of species including Drosophila melanogaster. rasiRNA itself is a short RNAs which participate in transposon transcription repression and mRNA degradation. Defects in rasiRNA system lead to increased transposition rate and developmental abnormalities due to accumulation of double-strand DNA breaks in fruitfly testes and ovaries. A number of proteins participate in rasiRNA-mediated repression including SPN-E (homeless), PIWI and ARMI. Mutations in the genes of these proteins lead to significant mobile element mRNA accumulation. We performed microarray-based study of effects of spn-E mutation on expression in fruitfly ovaries - one of the organs where rasiRNA system work. Our goal was the identification of other (besides mobile elements) targets of rasiRNA system regulation Total RNA samples, extracted from ovaries of spn-E1/spn-Ehls03987 trans-heterozygotes and mix of heterozygotes spn-E1/TM3 and spn-Ehls03987/TM3 (spn-E/+ hereafter), were reverse transcribed, IVT-amplified and labeled with Cy3 or Cy5. Mix of differently labeled aRNAs (spn-E1/spn-Ehls03987 - target, spn-E/+ - reference) was hybridized to Oligo14Kv2 microarray slides (CDMC), washed, scanned and treated in GenePix 6 (Molecular Devices) and subsequently in FlexArray 1.6.1.1 (McGill University and GM-CM-)nome QuM-CM-)bec Innovation Centre). Three biological replica (one sample dye-swapped) were produced and analyzed.

2013-03-11 | E-GEOD-40768 | biostudies-arrayexpress

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