Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Seq of P. aeruginosa clinical isolate collection

ABSTRACT: Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as antimicrobial resistance, biofilm formation or virulence Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE123544 | GEO | 2019/04/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of P. aeruginosa clinical isolate collection under biofilm growth conditions

Project description:Purpose : The goal of this study was to use RNA-seq to compare transcriptional profiles under biofilm conditions with planktonic growth and explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as biofilm structure or virulence. Methods : mRNA profiles were generated for Pseudomonas aeruginosa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device or paired end mode on an Illumina Novaseq 6000. mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using bowtie2 with default settings.

2020-01-21 | GSE134231 | GEO

Using RNA Seq to investigate adaptation mechanisms in P. aeruginosa

Project description:We demonstrate that the versatile environmental bacterium Pseudomonas aeruginosa adapts a virulence phenotype after serial passage in Galleria mellonella as an invertebrate model host. The virulence phenotype was not linked to the acquisition of genetic variations and was sustained for several generations, despite cultivation of the ex vivo virulence-adapted P. aeruginosa cells under non-inducing rich medium conditions. Transcriptional reprogramming seemed to be induced by a host-specific food source as reprogramming was also observed upon cultivation of P. aeruginosa in medium supplemented with polyunsaturated long-chain fatty acids. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from LB-cultures grown to an OD600 =2. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with defaut settings.

2019-07-08 | GSE122938 | GEO

Using RNA Seq to identify a CF habitat specific transcriptional profile

Project description:Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings.

2019-07-04 | GSE119356 | GEO

The DEAD-box RNA helicases RhlE2 is a global regulator of Pseudomonas aeruginosa lifestyle and pathogenesis

Project description:Purpose: We wanted to determine the transcriptome profile of PAO1 wild type, PAO1ΔrhlE1, PAO1ΔrhlE2 and PAO1ΔrhlE1ΔrhlE2 mutants on swarming conditions. Method: Cells were harvested using the RNA bacteria protect solution (QIAGEN). Total RNAs was extracted and purified using Monarch RNA isolation kit (NEB), treated with DNase I (Promega) three times to remove contaminating genomic DNA and re-purified again using phenol-chloroform. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 4000 device and mRNA reads were trimmed and mapped to the NC_002516.2(PAO1) reference genome from NCBI using Stampy pipeline with defaut settings.

2021-02-18 | GSE166986 | GEO

RNA Seq of passages of a small colony variant P. aeruginosa clinical isolate

Project description:Purpose : The goal of this study was to use RNA Seq to explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as colony morphology, c-di-GMP production and biofilm formation Methods : mRNA profiles were generated for Pseudomonas aerugionsa clinical samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.

2022-11-05 | GSE147921 | GEO

Adaptation of Pseudomonas aeruginosa to cultivation in standard laboratory conditions

Project description:We studied adaptation of the metabolically versatile bacterium Pseudomonas aeruginosa to standard laboratory conditions by propagating mismatch repair-deficient P. aeruginosa in exponential phase for 24 days in rich medium. In the selective environment of this large-bottleneck mutation accumulation experiment, the bacteria developed shorter lag phases, higher growth rates and higher maximum cell densities. Transcriptional profiling and phenotyping for growth in different media revealed that higher fitness under laboratory conditions evolved via different pathways. Although common adaptive mutations or mutations that define trade-offs were not identified, there was a convergent evolution of transcriptional profiles associated with a shift from biofilm-associated to planktonic lifestyles. Our results indicate that under constant planktonic conditions P. aeruginosa uses several genetic pathways in order to fine-tune adaptation towards faster growth. The selected mutations in the different genetic pathways show a great variety of biofilm, virulence and motility phenotypic trade-offs, thus implying that on the population level, the adaptation of P. aeruginosa to constant conditions does not compromise its versatility. Methods: mRNA profiles were generated for Pseudomonas aeruginosa samples derived from LB-cultures grown to an OD600 =0.4-0.6. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using Stampy pipeline with default settings.

2020-11-26 | GSE146906 | GEO

Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates

Project description:Purpose : The goal of this study was to use RNA Seq to explore the success of lasR mutants in the opportunistic pathogen Pseudomonas aeruginosa in a clinical context by profiling the functional consequences of patho-adaptive mutations in clinical isolates. Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples by deep sequencing.Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end mode; 2 x 50 bp) and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.

2022-02-23 | GSE191103 | GEO

Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis [50 strains]

Project description:Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations. Methods: We chose a subset of isolates from the sequenced population of 2,101 emm28 strains that would approximately span the genetic variation present in the entire population. Fifty emm28 strains were grown in triplicate, harvested at two time points, mid-exponential (ME) and early-stationary (ES) phases of growth, and assayed in triplicate by RNA-seq. rRNA was depleted using the Ribo-Zero rRNA removal kit for Gram-positive bacteria (Illumina) and libraries were made using the ScriptSeq complete kit for bacteria (Illumina). The cDNA libraries were prepared with indexed reverse primers from the ScriptSeq Index PCR primers kit (Illumina), and purified with AMPureXP beads (Beckman Coulter).

2018-12-31 | GSE113056 | GEO

Constant production of FlhG ensures proper function of the flagellar counter in Shewanella putrefaciens

Project description:Purpose : Identification of the regulons directly and indirectly affected by the main regulators of flagellation in Shewanella putrefaciens CN-32 Methods : mRNA profiles were generated for Shewanella putrefaciens CN-32 samples by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with default settings and mapped to the NC_009438.1 (Shewanella putrefaciens CN-32) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with default settings for single-end sequencing.

2022-12-21 | GSE207531 | GEO

RNA-seq in Arabidopsis thaliana Col and hcr2 mutant

Project description:RNA-prep of Col and hcr2 mutant from seedling and bud sample. RNA extracted by Trizol and cDNA was synthesized by using the ScriptSeq v2 RNA-seq Library Preparation Kit (SSV21124, Epicentre). ScriptSeq Index PCR Primers (RSBC10948, Epicentre) were used for library construction.

2022-03-23 | E-MTAB-10791 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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