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Rattus norvegicus

ABSTRACT: The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome.

PROVIDER: PRJNA373851 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5240060.fastq.gz	Fastqsanger.gz
	SRR5240057.fastq.gz	Fastqsanger.gz
	SRR5240058.fastq.gz	Fastqsanger.gz
	SRR5240059.fastq.gz	Fastqsanger.gz

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The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome.

Project description:The differential gene expressions of rat mucosa colonized with single or multi-species of MRSA or PA were studied using RNA-sequencing of total transcriptome. In multi-species in-vitro biofilms PA partially inhibited SA growth. However, no significant inhibition of MRSA was detected during in-vivo colonization of multi-species in rat bullae. A total of 1797 genes were significantly (p < 0.05) differentially expressed in MRSA or PA or MRSA+PA colonized rat middle ear mucosa with respect to the control. The poly-microbial colonization of MRSA and PA induced the differential expression of a significant number of genes that are involved in immune response, inflammation, signaling, development, and defense; these were not expressed with single species colonization by either MRSA or PA. Genes involved in defense, immune response, inflammatory response, and developmental process were exclusively up-regulated, and genes that are involved in nervous system signaling, development and transmission, regulation of cell growth and development, anatomical and system development, and cell differentiation were down-regulated after multi-species inoculation.

2018-01-15 | GSE94722 | GEO

Rattus norvegicus breed:Sprague Dawley

Project description:Differential gene expression of rat middle ear mucosa colonized with MRSA or Pseudomonas aeruginosa single species or multi-species

| PRJNA369443 | ENA

Transcription profiling of S. aureus to investigate an outbreak of severe infections with community-acquired methicillin-resistant Staphylococcus aureus carrying the Panton-Valentine leukocidin following immunization - duplicate of E-BUGS-45

Project description:BACKGROUND: Infections with community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) are emerging worldwide. We investigated an outbreak of severe CA-MRSA infections in children following out-patient vaccination. METHODS AND FINDINGS: We carried out a field investigation after adverse events following immunization (AEFI) were reported. We reviewed the clinical data from all cases. S. aureus recovered from skin infections and from nasal and throat swabs were analyzed by pulse-field gel electrophoresis, multi locus sequence typing, PCR and microarray. In May 2006, nine children presented with AEFI, ranging from fatal toxic shock syndrome, necrotizing soft tissue infection, purulent abscesses, to fever with rash. All had received a vaccination injection in different health centres in one District of Ho Chi Minh City. Eight children had been vaccinated by the same health care worker (HCW). Deficiencies in vaccine quality, storage practices, or preparation and delivery were not found. Infection control practices were insufficient. CA-MRSA was cultured in four children and from nasal and throat swabs from the HCW. Strains from children and HCW were indistinguishable. All carried the Panton-Valentine leukocidine (PVL), the staphylococcal enterotoxin B gene, the gene complex for staphylococcal-cassette-chromosome mec type V, and were sequence type 59. Strain HCM3A is epidemiologically unrelated to a strain of ST59 prevalent in the USA, although they belong to the same lineage. CONCLUSIONS: We describe an outbreak of infections with CA-MRSA in children, transmitted by an asymptomatic colonized HCW during immunization injection. Consistent adherence to injection practice guidelines is needed to prevent CA-MRSA transmission in both in- and outpatient settings. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-45

2009-01-16 | E-BUGS-45 | biostudies-arrayexpress

Differential gene expressions for androgen-induced benign prostatic hyperplysia rat underwent oral treatment of metabolic peptide ghrelin

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Project description:RNAseq of intestinal epithelial cells from ASF Mice colonized with a consortium of mucosa associated fungi

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Project description:Gene expression and phenotypic consequences of laboratory housing in rats. Disease related-phenotypes and associated gene expressions of sedentary animals (living solely in a standard cage) were compared with animals that had access to twice-weekly one-hour physical activity in a large box (PA) and with those that had access to voluntary running wheel exercise (EX). Experiment Overall Design: The left ventricle of 16 month female Sprague-Dawley rats was used for RNA extraction and hybridization on Affymetrix GeneChip Rat Genome 230 2.0 Arrays. Twelve animals from each treatment group (SED, PA, and EX) were used for microarray analysis (4 animals pooled per GeneChip).

2007-11-29 | E-GEOD-5085 | biostudies-arrayexpress

Htt14A2.5 induced verses uninduced

Project description:Htt14A2.5 is a clonal rat pheochromocytoma (PC12) cell line, that expresses a truncated form of expanded repeat Htt exon 1 protein fused at the C-terminus to enhanced green fluorescent protein (EGFP). For total RNA preparation, ~3 x 105 cells were plated on 150 mm plates and the following day either induced with 5 microM PA or treated with ethanol alone (uninduced) for 48 hrs followed by direct lysis using the RNeasy total RNA prep as described by the manufacturer (Qiagen, Valencia, CA). Cells were harvested at approximately 40-60% confluency. RNA was quantitated spectrophotometrically and integrity tested by capillary electrophoresis (Agilent 2100 Bioanalyzer). 25 micrograms total RNA was used to generate target cRNAs for hybridization to Affymetrix Rat Genome U34A oligonculeotide arrays (UCI DNA Array Core Facility). Four separate cell growths were performed for the PA induced verses uninduced comparisons. Target cRNA was synthesized separately for each of these cell growths and hybridized individually to the oligonucleotide microarrays. Keywords = huntingtin Keywords = PC12 Keywords: repeat sample

2005-05-30 | GSE2602 | GEO

Sputum exosomal microRNAs profiling reveals critical pathways modulated by Pseudomonas aeruginosa colonization in bronchiectasis

Project description:Our findings have clinical implications. Identification of sputum exosomal miRNA helps explore the important biological pathways underlying the pathogenesis of bronchiectasis, thus unraveling candidate targets for future interventions of PA colonization. Apart from canonical inflammatory pathways, we have unraveled the modulation of longevity regulation pathway which opens a new avenue for exploring how PA colonization interacts with the airway epithelium. The significant correlation between sputum inflammatory biomarkers and miR-92b-5p and miR-223-3p provided further evidence on the unresolved inflammation in the PA-colonized microenvironment. However, causality cannot be inferred based on the current study design.

2022-01-01 | GSE138820 | GEO

Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium

Project description:Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Δvwbp and ΔscpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation.

2015-12-31 | GSE47910 | GEO

Next-generation sequencing facilitates quantitative analysis of miRNAs of cetuximab-resistant colorectal cancer (HCT116-R) cells

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2021-08-13 | GSE181843 | GEO

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