Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Pseudomonas aeruginosa PAO1 wild-type and mutant containing a single nucleotide polymorphism in fusA1

ABSTRACT: The gene encoding elongation factor G, fusA1, is frequently mutated in clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis. Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the aminoglycoside efflux pump, MexXY. We isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1-P443L) in which mexXY expression was increased. We compared the transcriptome of this fusA1 mutant (EMC1) with the P. aeruginosa PAO1-derived progenitor strain (EMC0) and complemented mutant strain expressing the wild-type fusA1 gene in trans (EMC1*).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Pseudomonas aeruginosa PAO1

SUBMITTER: Eve Maunders

PROVIDER: E-MTAB-8690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol, MOPS Acetate

Project description:Drastic alterations in transcripts associated with central carbon metabolism and associated processes have been repeatedly observed a common expression program as P. aeruginosa adapts to the cystic fibrosis lung when compared to standard laboratory conditions. However, we have limited knowledge of how well these transcriptomic changes correlate with actual alterations in metabolic flux; the rate of turnover of molecules through metabolic pathways. We have compared the transcriptome of Pseudomonas aeruginosa PAO1 during growth on the carbon sources acetate and glycerol.

2019-10-05 | E-MTAB-8374 | biostudies-arrayexpress

Pseudmonas aeruginosa PAO1 wild-type cultured in MOPS Glycerol compared to MOPS Glycerol Hypoxia (restricted oxygen).

Project description:Pseudmonas aeruginosa PAO1 wild-type cultured in MOPS Glycerol compared to MOPS Glycerol Hypoxia (restricted oxygen). P. aeruginosa strain PAO1 was grown in 40 ml MOPS with glycerol as sole carbon source (triplicate), 37 °C with shaking (250 rpm) in baffled flasks (500 ml). For the restricted oxygen condition, P. aerugionosa was cultured in the same conditions, except non-baffled flasks were used, and the shaking speed was 80 rpm (gentle aggitation). A thin layer 10 ml of mineral oil was overlaid on top of these cultures to restrict oxygen transfer.

2019-12-02 | E-MTAB-8442 | biostudies-arrayexpress

Pseudmonas aeruginosa PAO1 wild-type and delta prpC cultured on MOPS Succinate and MOPS Succinate + Propionate

Project description:Pseudomonas aeruginosa strain PAO1 (wild-ype and prpC) was grown in 40 ml MOPS with succinate as the sole carbon source, 37 °C with shaking (250 rpm) in baffled flasks (500 ml). During exponential growth, 500 uM propionate was added to the cultures (H2O added to controls). Samples were harvested during mid-exponential growth. Four conditions, 12 samples total (triplicate). 5 ml of culture was harvested from each sample and added to an equal volume of RNAlater® RNA stabilization solution. Samples were then centrifuged at 4000 rpm for 15 min (4 °C) and the pellets were stored at – 80 °C. RNA was extracted using a RNAeasy Mini-Kit according to the manufacturers instructions. RNA was estimated with a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies Inc, USA) and using agarose gel electrophoresis. Ribosomal RNA (rRNA) was then depleted from each sample (5 µg each) using the bacterial Ribo-Zero rRNA Removal Kit (Illumina). The integrity of the RNA was evaluated using an RNA 6000 Nano LabChip and an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany). Eight indexed, strand-specific cDNA libraries were prepared, and samples were sequenced on an Illumina HiSeq 2000 with a 51-bp single-end read length (GATC Biotech, Germany).

2021-11-01 | E-MTAB-10077 | biostudies-arrayexpress

Proteome of Pseudomonas aeruginosa PAO1 wild-type and mutant containing a single nucleotide polymorphism in fusA1

Project description:The gene encoding elongation factor G, fusA1, is frequently mutated in clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis. Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the aminoglycoside efflux pump, MexXY. We isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1-P443L) in which mexXY expression was increased. We compared the proteome of this fusA1 mutant (EMC1) with the P. aeruginosa PAO1-derived progenitor strain (EMC0) and complemented mutant strain expressing the wild-type fusA1 gene in trans (EMC1*).

2020-09-16 | PXD017266 | Pride

The Candida albicans regulator ZCF21 controls the expression of cell wall components

Project description:We report that a transcriptional regulator that originated in the lineage that gave rise to multiple host-associated Candida species is a key component of the circuitry that governs the C. albicans cell surface composition. Specifically, we show that the transcription regulator ZCF21 controls the expression of genes encoding multiple cell surface proteins and cell wall modifying enzymes. Transcriptome (RNA-seq) analysis of 2 Candida albicans strains (reference strain and zcf21 deletion mutant) grown under 4 culture conditions (YPD broth at 30Â°C for 24h; YPD broth at 30Â°C in the presence of 15 mM caffeine for 24h; Todd-Hewitt agar at 37Â°C for 24h; Todd-Hewitt agar at 37Â°C for 24h in the presence of 5 mM caffeine).

2015-11-01 | E-GEOD-73373 | biostudies-arrayexpress

Transcriptomic profiling of three different neuroblastoma cell lines (CLB-BAR, CLB-GE and SK-N-AS) in response to ALK inhibition

Project description:Anaplastic Lymphoma Kinase (ALK) is a tyrosine kinase receptor which is a clinical target of major interest in cancer, including neuroblastoma. To better understand ALK signaling, three different neuroblastoma cell lines (CLB-BAR, CLB-GE and SK-N-AS) were cultured for 1hr and 24hrs in control conditions or after treatment with the ALK inhibitors crizotinib or lorlatinib. RNA-Seq experiments were performed to determine the expression changes resulting from ALK inhibition. Together with parallel phosphoproteomic experiments, these data unveil several important conserved oncogenic pathways in neuroblastoma.

2018-09-01 | E-MTAB-6654 | biostudies-arrayexpress

Aspergillus fumigatus in blood reveals a "just wait and see" resting stage behavior

Project description:Objective: We analyzed changes in A. fumigatus gene expression profile at various stages of an in vitro model of aspergillosis to study the adaptation of A. fumigatus to the blood environment. Results: Most of virulence factors described to be involved in aspergillosis were not activated during the blood phase. We found three active processes to be activated in the later phase that may help to the adaptation: Iron homeostasis, a partial secondary metabolite cluster and the formation of detoxification enzymes. Conclusions: We propose that A. fumigatus is unable to grow in blood and it requires a metabolic change that allows the organism to shut down all uptake and energy-consume mechanisms, resulting in a resting mycelial stage. We performed gene expression profile by sequencing mRNA of A. fumigatus that were growm under two conditions, Minimal Medium (M) and human blood (B), and at different times: before placing the fungus in the final medium (pre), at 30' and at 180', with 2 biological replicates per condition.

2015-11-24 | E-GEOD-70227 | biostudies-arrayexpress

Transcriptomic changes in aquaporin PIP1;2 deficient Arabodposis plants

Project description:The leaf transcriptome of the Arabidopsis thaliana aquaporin gene PIP1;2 T-DNA insertion line was compared to that of control plants. In total 730 genes were found to be differentially regulated. This regulation pattern was compared to mild drought stress and low CO2 Affymetrix data to elucidate whether loss of the aquaporin resembles transcriptomic changes of drought stress or lack of CO2 supply. Mild drought stress data were obtained from Harb A, Krishnan A, Ambavaram MMR, Pereira A (2010) Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth. Plant Physiology 154: 1254-1271 (GSE24177). Low CO2 data were obtained from Oliver E. Bläsing, Yves Gibon, Manuela Günther, Melanie Höhne, Rosa Morcuende, Daniel Osuna, Oliver Thimm, Björn Usadel, Wolf-Rüdiger Scheible, and Mark Stitt (2005) Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis. The Plant Cell, Vol. 17, 3257-3281 (GSE3423). 2 samples examined: wildtype and atpip1;2-1 mutant

2015-01-10 | E-GEOD-34984 | biostudies-arrayexpress

RNA-seq of coding RNA from cluster roots (pre-emergent, juvenile and mature) from Lupinus albus grown for 20 days under phosphorus-deficiency

Project description:RNA-seq analysis was performed on different developmental stages of cluster roots (pre-emergent, juvenile and mature) from Lupinus albus grown for 20 days under phosphorus-deficiency

2014-07-01 | E-MTAB-2253 | biostudies-arrayexpress

Lotus japonicus response to Nod factor: wild type and nfre mutants

Project description:For RNA sequencing, 3 days seedlings were moved to agar plates supplemented with 1/4 B&D media and susceptible zone of 14 days-old plants was harvested after specific treatment with water (Mock treated) or M.loti Nod factor 10-8M (NF). The total RNA was isolated from the susceptible zone (15 mm root pieces) using Nucleo spin RNA plant (Macherey-Nagel). Total RNA (> 0.8 g) from two biological replicas per sample was used by GATC Biotech (Germany) to prepare random primed cDNA library and for sequencing with Illumina HiSeq: read length 1 x 50bp. Gifu- L. japonicus wild-type, 4820- nfre-1 allele of Nfre, 38534- nfre-2 allele of Nfre.

2018-06-27 | E-MTAB-5855 | biostudies-arrayexpress

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