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RNAseq of Pseudomonas extremaustralis treated with GSNO at low oxygen conditions (treated sample and controls)

ABSTRACT: RNAseq of Pseudomonas extremaustralis treated with GSNO at low oxygen conditions (treated sample and controls)

PROVIDER: PRJEB52622 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9681654.fastq.gz	Fastqsanger.gz
	ERR9681655.fastq.gz	Fastqsanger.gz
	ERR9681656.fastq.gz	Fastqsanger.gz
	ERR9681657.fastq.gz	Fastqsanger.gz

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RNAseq of Pseudomonas extremaustralis treated with GSNO at low oxygen conditions (treated sample and controls)

Project description:Pseudomonas extremaustralis, an Antarctic bacterium, was grown at low oxygen conditions for 24h and then exposed to S-Nitrosoglutathione (GSNO)100 µM for 1 h. RNA from treated and control samples was isolated using the Trizol method. RNA quality was analyzed on the Agilent Bioanalyzer and rRNA depletion was performed using the RiboZERO kit (Illumina). Samples were validated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced with the Illumina NextSeq 550 platform with a single-end protocol.

2024-03-15 | E-MTAB-11689 | biostudies-arrayexpress

RNAseq of Pseudomonas extremaustralis under oxidative stress at low oxygen conditions

Project description:Pseudomonas extremaustralis an Antarctic bacterium was grown at low oxygen conditions and exposed to oxidative stress during 1 hour. Experimental and control samples were analyzed by RNA-seq experiments.

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RNAseq of Pseudomonas extremaustralis under oxidative stress at low oxygen conditions

Project description:RNAseq of Pseudomonas extremaustralis under oxidative stress at low oxygen conditions

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RNA-seq of Pseudomonas extremaustralis/pBAD18-sRNA40 and P. extremaustralis/pBAD18 strain

Project description:sRNA40 (a novel sRNA) was pulse-expressed and its effects studied by transcriptomic profiling in P. extremaustralis, an Antarctic bacterium. For this approach we built a plasmid-based system, where sRNA40 was cloned under the control of the heterologous araBp promoter, inducible by arabinose (pBAD18-sRNA40). P. extremaustralis carrying the empty plasmid pBAD (pBAD18) was used as a control. Both strains were grown at low oxygen conditions for 24 hours. Cells were harvested after 10 min of induction with 0.1% arabinose. RNA was isolated using the Trizol method. RNA quality was analyzed on the Agilent Bioanalyzer and rRNA depletion was performed using the RiboZERO (Illumina). Samples were validated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced with the Illumina NextSeq 550 platform with a single-end protocol.

2023-04-29 | E-MTAB-10406 | biostudies-arrayexpress

Pseudomonas extremaustralis

Project description:Pseudomonas extremaustralis overview

| PRJNA78109 | ENA

RNA-seq of Pseudomonas extremaustralis/pBAD18-sRNA40 and P. extremaustralis/pBAD18 strain

Project description:RNA-seq of Pseudomonas extremaustralis/pBAD18-sRNA40 and P. extremaustralis/pBAD18 strain

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Transcriptional response of Candida parapsilosis in low oxygen (hypoxic) conditions in SD media

Project description:Whole genome microarray was used to compare the transcriptional profile of C. parapsilosis growing in normoxic (21% oxygen) and hypoxic (1% oxygen) conditions.

2009-01-15 | GSE13722 | GEO

Differential responses of choroidal melanocytes and uveal melanoma cells to low oxygen conditions

Project description:PURPOSE: Tissue culture is traditionally performed at atmospheric oxygen concentration (21%), which induces hyperoxic stress, as endogenous physiologic oxygen tension found in tissues varies between 2% and 9%. This discrepancy may lead to misinterpretation of results and may explain why effects observed in vitro cannot always be reproduced in vivo and vice versa. Only a few studies have been conducted in low physiologic oxygen conditions to understand the development and differentiation of cells from the eye. METHODS: The aim of this study was to investigate the growth and gene expression profile of melanocytes from the choroid permanently exposed to 21% (hyperoxic) or 3% (physiologic) oxygen with proliferation assays and DNA microarray. The cellular behavior of the melanocytes was then compared to that of cancer cells. RESULTS: The gross morphology and melanin content of choroidal melanocytes changed slightly when they were exposed to 3% O2, and the doubling time was statistically significantly faster. There was an increase in the percentage of choroidal melanocytes in the active phases of the cell cycle as observed by using the proliferation marker Ki67. The caveolin-1 senescence marker was not increased in choroidal melanocytes or uveal melanoma cells grown in hyperoxia. In comparison, the morphology of the uveal melanoma cells was similar between the two oxygen levels, and the doubling time was slower at 3% O2. Surprisingly, gene expression profiling of the choroidal melanocytes did not reveal a large list of transcripts considerably dysregulated between the two oxygen concentrations; only the lactate transporter monocarboxylate transporter (MCT4) was statistically significantly upregulated at 3% O2. CONCLUSIONS: This study showed that the oxygen concentration must be tightly controlled in experimental settings, because it influences the subsequent cellular behavior of human choroidal melanocytes.

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