Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22016502_1.fastq.gz | Fastqsanger.gz | |||
| SRR22016502_2.fastq.gz | Fastqsanger.gz | |||
| SRR22016503_1.fastq.gz | Fastqsanger.gz | |||
| SRR22016503_2.fastq.gz | Fastqsanger.gz | |||
| SRR22016504_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:Previous studies have documented the diversity of genetic background of methicillin-resistant S. aureus (MRSA) strains associated with healthcare (HA-MRSA), community (CA-MRSA) and livestock (LA-MRSA). The accessory and core-variable genome content of those strains remain largely unknown. To compare the composition of accessory and core-variable genome of Belgian MRSA strains according to host, population setting and genetic background, representative strains of HA- (n=21), CA- (n = 13) and ST398 LA-MRSA (n = 18) were characterized by a DNA-microarray (StaphVar Array) composed of oligonucleotide probes targeting ~400 resistance, adhesion and virulence associated genes.ST398 strains displayed very homogenous hybridization profiles (>94% gene content homology) irrespective of their host origin. This “ST398-specific” genomic profile was not distantly demarked from those of certain human-associated lineages but lacked several virulence- and colonization-associated genes harbored by strains of human origin, such as genes encoding proteases, haemolysins or adhesins. No enterotoxin gene was found among ST398 strains. In conclusion, our findings are consistent with a non-human origin of this ST398 lineage but suggest that it might have the potential to adapt further to the human host.
2010-11-15 | GSE20541 | GEO
Project description:LA-MRSA
| PRJEB62143 | ENA
Project description:<h4><strong>BACKGROUND: </strong>The introduction of high-risk human papillomavirus (hrHPV) testing as part of primary cervical screening is anticipated to improve sensitivity, but also the number of women who will screen positive. Reflex cytology is the preferred triage test in most settings but has limitations including moderate diagnostic accuracy, lack of automation, inter-observer variability and the need for clinician-collected sample. Novel, objective and cost-effective approaches are needed.</h4><h4><strong>METHODS: </strong>In this study, we assessed the potential use of an automated metabolomic robotic platform, employing the principle of laser-assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) in cervical cancer screening.</h4><h4><strong>FINDINGS: </strong>In a population of 130 women, LA-REIMS achieved 94% sensitivity and 83% specificity (AUC: 91.6%) in distinguishing women testing positive (n = 65) or negative (n = 65) for hrHPV. We performed further analysis according to disease severity with LA-REIMS achieving sensitivity and specificity of 91% and 73% respectively (AUC: 86.7%) in discriminating normal from high-grade pre-invasive disease.</h4><h4><strong>INTERPRETATION: </strong>This automated high-throughput technology holds promise as a low-cost and rapid test for cervical cancer screening and triage. The use of platforms like LA-REIMS has the potential to further improve the accuracy and efficiency of the current national screening programme.</h4><h4><strong>FUNDING: </strong>Work was funded by the MRC Imperial Confidence in Concept Scheme, Imperial College Healthcare Charity, British Society for Colposcopy and Cervical Pathology, National Research Development and Innovation Office of Hungary, Waters corporation and NIHR BRC.</h4>
2022-02-15 | MTBLS1371 | MetaboLights
Project description:Studies on S. aureus sub-populations revealed that genomes are well conserved between isolates from the same lineages despite geographic, temporal and selective diversity. However, variation of hundreds of genes can occur between isolates from different lineages and these genes could be involved in interaction with host components. In this study, we aimed to investigate the diversity of secreted virulence factors in human and zoonotic S. aureus isolates from different clonal complexes. We focused on the S. aureus clonal complexes (CC) 8 and CC22 as dominant human lineages, and CC398 as dominant livestock-associated MRSA (LA-MRSA) which is disseminating rapidly. To study the diversity of secreted virulence factors, we compared their extracellular proteomes using label-free LC-MS/MS analysis. A common protein database was created based on DNA sequencing data and PAN genome IDs.
2018-09-11 | PXD008797 | Pride
Project description:Methicillin-resistant Staph. Aureus (MRSA) is a common cause of severe pneumonia and sepsis that can lead to Acute Respiratory Distress Syndrome (ARDS). MRSA causes lung endothelial cell (EC) dysfunction, a critical step in the pathogenesis and progression of lung injury. Our previous studies have demonstrated that FTY720 S-phosphonate (Tysiponate, Tys), an analog of sphingosine-1-phosphate, ameliorates MRSA-induced lung EC activation and barrier disruption (PMID: 35015568). To advance our mechanistic understanding of MRSA and Tys effects on lung EC, we investigated associated epigenetic changes. Specifically, we studied histone lysine acetylation, which is a central epigenetic alteration that has been linked to gene transcription and functional regulation of endothelial responses to inflammatory stimuli. We therefore determined the effects of MRSA exposure in the presence or absence of Tys on lung EC acetylation at the 9th lysine residue of the histone H3 protein (H3K9ac), which is an important chromatin modification associated with active promoters and gene activation. ChIP-seq analysis was employed to perform an unbiased genome-wide profiling of H3K9ac epigenetic patterns in human lung EC. This analysis identified multiple genes that are differentially targeted by acetylation when EC are exposed to MRSA±Tys.
2025-01-28 | GSE274958 | GEO
Project description:The recently identified histone modification lysine lactylation can be stimulated by L-lactate and glycolysis. Although the chemical group added upon lysine lactylation was originally proposed to be the L-enantiomer of lactate (KL-la), two isomeric modifications, lysine D-lactylation (KD-la), and N-ε-(carboxyethyl) lysine (Kce), also exist in cells, with their precursors being metabolites of glycolysis. The dynamic regulation and differences among these three modifications in response to hypoxia have not been investigated previously. In this study, we demonstrate that intracellular KL-la, but not KD-la or Kce, is upregulated in response to hypoxia. Depletion of glyoxalase enzymes, GLO1 and GLO2, had minimal impact on KD_x001E_la, Kce, or hypoxia-induced KL-la. Conversely, blocking glycolytic flux to L-lactate under hypoxic conditions by knocking out LDHA/B completely abolished the induction of KL-la, but increased KD-la and Kce. We further observed a correlation between the level of KL-la and HIF-1α expression under hypoxic conditions and when small molecules were used to stabilize HIF-1α in the normoxia condition. Our result demonstrated that there is a strong correlation between HIF-1α and KL-la in lung cancer tissues, and that patient samples with higher grade tend to have higher KL-la levels. Using a proteomics approach, we quantified 66 KL-la sites that were upregulated by hypoxia and demonstrated that p300/CBP contributes to hypoxia-induced KL-la. Collectively, our study demonstrates that KL-la, rather than KD-la or Kce, is the prevailing lysine lactylation in response to hypoxia. Our results therefore demonstrate a link between KL-la and the hypoxia-induced adaptation of tumor cells.
2025-02-10 | GSE285693 | GEO