Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Changes in expression of small non-coding RNAs, including microRNAs, in response to stress in C. elegans

ABSTRACT: To investigate the contribution of small non-coding RNAs, including microRNAs, to stress response in C. elegans, we examined their expression changes using Illumina deep-sequencing technology. Stress conditions we examined include heat shock, Pseudomonas aeruginosa (PA-14) and L1 arrest. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE25739 | GEO | 2010/12/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Changes in expression of small non-coding RNAs, including microRNAs, in response to stress in C. elegans

Project description:To investigate the contribution of small non-coding RNAs, including microRNAs, to stress response in C. elegans, we examined their expression changes using Illumina deep-sequencing technology. Stress conditions we examined include heat shock, Pseudomonas aeruginosa (PA-14) and L1 arrest. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Total RNAs were purified from wild-type young adult animals that were exposed to each stress condition, and used for cDNA library preparation for small RNAs. As for the L1 arrest sample, first wild-type embryos were collected and cultured without a food source in M9 buffer for 48 hrs with rotation, and then RNAs purified from L1 animals in a developmentally arrested state were used for the library preparation. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.

2010-12-02 | E-GEOD-25739 | biostudies-arrayexpress

Gene expression profile of human lung tissue explants infected with bacteria/virus by RNAseq

Project description:RNA-seq was performed to study the transcriptomic changes in human lung tissue post infection with either Influenza A virus (IAV), or Pseudomonas aeruginosa (PA) or Mycobacterium bovis (BCG)

2021-12-30 | GSE192528 | GEO

Galectin-8 downmodulates TLR4 activation and impairs bacterial clearance in a mouse model of Pseudomonas keratitis

Project description:In our study, we used a mouse model infected with Pseudomonas aeruginosa (PA) to provoke a painful, sight-threatening corneal infection. FACS sorted WT and Gal-8-/- neutrophils of PA infected corneas were processed for next-generation transcriptomic RNA sequencing (RNA-seq).

2022-12-03 | E-MTAB-12376 | biostudies-arrayexpress

small non-coding RNA expression profile of human lung tissue explants infected with bacteria/virus by RNAseq

Project description:small non-coding RNA-seq was performed to study the transcriptomic changes in human lung tissue post infection with either Influenza A virus (IAV), or Pseudomonas aeruginosa (PA) or Mycobacterium bovis (BCG)

2022-01-04 | GSE192864 | GEO

Microarray analysis of effect of N-(3-oxo-dodecanoyl) homoserine lactone on S. cerevesiae

Project description:We examined whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes, specifically a variety of quorum sensing molecules from different bacteria species and from Candida albicans. We found that only N-acyl-3-oxo-dodecanoyl homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a stress response in yeast. Microarray experiments were performed in order to continue investigating the stress response. We treated S. cerevesiae (WT strain W303) with N-(3-oxo-dodecanoyl) homoserine lactone (C12), a quorum sensing molecule of Pseudomonas aeruginosa, which we found causes a stress response using a GFP reporter for HSP-12. Treatment conditions: 100 uM C12, 100 uM C12-lactam (control: synthetic analogue of C12 that is inactive in P. aeruginosa), DMSO (control: solvent), and 0.3 mM H2O2 (for comparison to oxidative stress).

2020-03-02 | E-MTAB-4802 | biostudies-arrayexpress

Exploring roles of the chitinase ChiC in modulating Pseudomonas aeruginosa virulence phenotypes

Project description:Chitinases are ubiquitous enzymes involved in biomass degradation and chitin turnover in nature. Pseudomonas aeruginosa (PA), an opportunistic human pathogen, expresses ChiC, a secreted glycoside hydrolase 18 (GH18) family chitinase. Despite speculation about ChiC's role in PA disease pathogenesis, there is scant evidence supporting this hypothesis. Since PA cannot catabolize chitin, we investigated the potential function(s) of ChiC in PA pathophysiology

2024-04-30 | PXD048320 | Pride

Exploring roles of the chitinase ChiC in modulating Pseudomonas aeruginosa virulence phenotypes

2024-04-30 | PXD048596 | Pride

RNA Sequencing of unc-30(ok613) and wild type (WT) N2 C. elegans in Pseudomonas aeruginosa (PA14) infection

Project description:Purpose: To uncover immune mediated genes and pathways by Pseudomonas aeruginosa infection that are modulated by the homeodomain PITX1/UNC-30, which plays a vital role in the GABAergic signaling in C. elegans Methods: RNA was extracted from synchronized Pseudomonas aeruginosa infected L4 stage unc-30(ok613) and WT using Qiagen extraction kits and following standard methods. The animals were grown on OP50 at 20 C and infected at 25 C. Results: RNA seq analyses shows enriched and signficant Pseudomonas aeruginosa mediated upregulated immune, neuropeptide and metabolism genes and pathways that are dependent of GABAergic signaling Conclusions: Our study uncovered GABAgergic signaling to be modulator of the innate immunity in C elegans during Pseudomonas aeruginosa infection

2021-01-31 | GSE149862 | GEO

The architecture and pathogenesis of Pseudomonas-Candida biofilms in infections and their influence on the microenvironment

Project description:Interkingdom Pseudomonas-Candida biofilms is a human pathogen associated with acute and chronic infection. This study examine hoe their structural organization influences their in vivo microenvironment, which in turns affects the interaction of Pseudomonas-Candida biofilms with host immune responses. NCI-H292 grown P. aeruginosa biofilms with and without C. albicans biofilms were used for proteomic analysis. Biofilms were demonstrated in all groups which have 357 proteins from proteomic analysis including i) proteins in PA+CA were higher than PA (76 proteins, such as sigma factor AlgU negative regulatory protein; MucA) and ii) proteins in PA+CA were lower than PA (281 proteins, including alginate genes such as Alginate biosynthesis transcriptional regulatory protein; AlgB). Although most of Pseudomonas proteins in PA+CA were lower than PA due to the lower initial bacteria in preparation of mixed-organism biofilms, mucA overexpressed in PA+CA indicating that high alginate production that transcriptionally controlled by algU-mucABCD genes. These results demonstrated that Pseudomonas-Candida biofilms produced alginate more compared to Pseudomonas biofilms on lungs.

2022-10-13 | PXD034528 | Pride

Oxoeicosanoid signaling promotes early antimicrobial defense in zebrafish (Danio rerio)

Project description:RNAseq was performed on hcar1-4+/+ and hcar1-4-/- zebrafish larvae with (2 h and 4 h) or without (0 h) Pseudomonas aeruginosa (PA) ear infection. The transcriptome profile generated here reveals PA14 infection-induced differential gene expression patterns between hcar1-4-/- and hcar1-4+/+ siblings.

2022-10-31 | GSE201604 | GEO

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