Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of arsenic and Pseudomonas aeruginosa infection on gene expression in human airway epithelial cells

ABSTRACT: Purpose: To determine effects of arsenic on gene expression in polarized primary human bronchial epithelial (HBE) cells and impact on transcriptional response to Pseudomonas aeruginosa infection Methods: mRNA profiles of HBE cells from 6 donors exposed to 0, 5, 10 or 50 ug/L total arsenic +/- Pseudomonas aeruginosa (48 samples) were generated using Illumina sequencing, aligned in CLC Genomics workbench and analyzed for DE in EdgeR Findings: 20-30 million reads were mapped per sample and transcripts were identifed that were significantly differentially expressed in response to arsenic and Pseudomonas aeruginosa

ORGANISM(S): Homo sapiens

PROVIDER: GSE97036 | GEO | 2017/06/26

SECONDARY ACCESSION(S): PRJNA380496

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms.

Project description:Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ?anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ?anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ?anr, clinical isolate J215, and J215 ?anr, each in duplicate, by deep sequencing using Illumina HiSeq.

2015-06-29 | E-GEOD-68534 | biostudies-arrayexpress

CARD9-associated Dectin-1 and Dectin-2 are Required for Protective Immunity of a Multivalent Vaccine Against Coccidioides posadasii Infection

Project description:Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module) were conducted at the Genomics Core of UT Health San Antonio. Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench. To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010). Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).

2020-04-16 | GSE133140 | GEO

Comprehensive analysis the effect of arsenic exposure on the virulence and antibiotic resistance of Pseudomonas aeruginosa

Project description:Natural or industrial pollution of source water by arsenic poses a serious threat to the health of tens of millions of people worldwide, while limited data have addressed its influence on the waterborne pathogens. This study examines the effects of arsenic exposure on Pseudomonas aeruginosa, an opportunistic pathogen that poses a health hazard in public water supplies. Our findings reveal that arsenic exposure at concentrations of 0.12–20 mg/L As(III) causes rapid growth arrest in P. aeruginosa. This exposure also leads to a marked decrease in elastase, pyocyanin, and flagellar production, while significantly increasing siderophore and extracellular polysaccharide production. Proteomic analysis indicates that both low (0.12 mg/L) and high (1.2 mg/L) arsenic levels trigger an antioxidant defense response, evidenced by the upregulation of Fnr-2, TrxB2, Ohr, AlgZ, and PslG. Concurrently, proteins related to basal metabolism, quorum sensing, T3SS, pyocyanin biosynthesis, and flagellar assembly are downregulated. Moreover, arsenic exposure enhances the expression of proteins involved in siderophore biosynthesis and transporters associated with iron uptake and multidrug resistance. In vitro assays further demonstrate that arsenic exposure reduces bacterial cytotoxicity while promoting survival and proliferation under antibiotic treatment. In summary, this study provides comprehensive insights into how arsenic affects bacterial virulence and antibiotic tolerance in P. aeruginosa, highlighting the potential public health risks posed by the frequent co-occurrence of arsenic-contaminated water sources and multidrug-resistant bacteria.

2024-08-20 | PXD055019 |

Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms.

Project description:Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ∆anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ∆anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters.

2015-06-29 | GSE68534 | GEO

Transcriptional response of Pseudomonas aeruginosa PAO1 to NaClO

Project description:In this experiment the transcriptional response of the opportunistic human pathogen Pseudomonas aeruginosa to sublethal concentrations of NaClO was investigated. To this aim, four independent cultures of P. aeruginosa PAO1 grown in minimal medium BM2 were treated with NaClO (2 ug/ml) for 1 h at 37 C followed by RNA extraction and microarray analysis. Untreated cultures served as controls.

2018-04-30 | E-MTAB-2876 | biostudies-arrayexpress

Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Monocyte-Depleted Brain Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived brain transcriptome profiling (RNA-seq) to reveal the difference of cellular pathways in adult brains of wild type (WT) and monocyte-depleted (CCR2-DTR) mice 8 days post infection of Trichinella spiralis. Methods: Illumina compatible RNAseq library was prepared using NEB next ultra RNAseq library preparation kit. The sequencing of the cDNA libraries was performed on the Illumina NextSeq platform (Illumina, San Diego, CA) using the high output 1X75 cycles configuration. CLC Genomics Workbench 11.0.1 version (http://www.clcbio.com/products/clc-genomics-workbench/ ; Qiagen) was used for RNA-seq analysis. De-multiplexed fastq files from RNA-Seq libraries are imported into the CLC software. Bases with low quality were trimmed and reads are mapped to reference genome Mus musculus genome GRCm38. The reference genome sequence and annotation files were downloaded from ENSEMBLE, release.92 (Mus_musculus.GRCm38.92.fa, and Mus_musculus.GRCm38.92.gtf). The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench. Statistical analysis of differentially expressed genes is carried out based on a negative binomial model using a tool in CLC Genomic Workbench. The reference genome sequence and annotation files were downloaded from ENSEMBL, release.92 (Mus_musculus.GRCm38.92.fa, and Mus_musculus.GRCm38.92.gtf). The aligned reads were obtained using the RNA-Seq Analysis Tool of CLC Genomics Workbench. Results: Using an optimized data analysis workflow, we mapped over 50 million sequence reads per sample to the mouse genome (GRCm38) and found that Trichinella-infected mice depleted of monocytes presented with significantly increased expression of proinflammatory genes compared to controls.

2022-08-25 | GSE190493 | GEO

Gene expression analysis on arsenic-induced malignant transformation

Project description:Arsenic is environmental risk factor and has been linked to urothelial carcinoma incidence. Arsenic exposure-induced malignant transformed cells was established from normal urothelial cells by chronic arsenic exposure for 10 months. The purpose of the present study is to elucidate the relevant molecular alterationon on arsenic-induced malignant transformation.

2016-11-19 | GSE90023 | GEO

Fremont et al 2023 - Arsenic stress triggers active exudation of arsenic-phytochelatin complexes from Lupinus albus roots

Project description:Arsenic stress triggers active exudation of arsenic-phytochelatin complexes from Lupinus albus roots

2023-10-10 | MSV000093078 | MassIVE

Arsenic-induced Changes in L2 Cells

Project description:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic alters gene expression leading to carcinogenesis in the lung. In this study, we examined global gene expression in response to 0.75 µM arsenic treatment for 1-7 days in a rat lung epithelial cell line (L2) using an in-house 10k rat DNA microarray. One hundred thirty one genes were identified using the one-class statistical analysis of microarray (SAM) test. Of them, 33 genes had a fold change of ≥ 2 at least between two time points. These genes were then clustered into 5 groups using K-means cluster analysis based on their expression patterns. Seven selected genes, all associated with cancer, were confirmed by real-time PCR. These genes have functions directly or indirectly related to metabolism, glycolysis, cell proliferation and differentiation, and regulation of transcription, all of which may be involved in neoplastic transformation of cells. Our findings provide important insight for the future studies of arsenic-mediated lung cancer. Keywords: Lung, aresenic, L2, micorarray

2011-12-23 | GSE9790 | GEO

Conformation/Identification of dPPRrcbL RNA targets using RIPSeq

Project description:Stroma extracts were isolated from 2-week-old transgenic dPPRrbcL or WT plants and incubated with HA-specific antibodies. IgGs were captured with Protein A Dynabeads (Thermo Fisher scientific) and recovered RNA was used for generation of libraries with the NEBNext® Ultra™ II RNA Library Prep Kit. Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench. Reads of the two replicates aligned in CLC Genomics Workbench were extracted as coverage (reads per nucleotide). Graphs were created with excel using the extracted coverage values

2021-02-28 | GSE146249 | 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