Proteomics of PAO1 subject to Pf4 superinfection or not
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas Aeruginosa Pao1
SUBMITTER: 
Mingxing Tang
PROVIDER: PXD068203 | iProX | Mon Sep 08 00:00:00 BST 2025
REPOSITORIES: iProX
Similar Datasets
Project description:We carried out globlal proteomics analysis on P. aeruginosa PAO1 and ΔodsR (ΔPA2076) strains to determine differences following treatment with OA, 10-HOME, or 7,10-DiHOME oxylipin vs non-treated controls.
2019-02-25 | PXD012256 | Pride
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of farnesol-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: Our RNA-seq results showed that less than 100 genes of P. aeruginosa PAO1 were differentially expressed following farnesol treatment. We found that about 1.7% of all detected genes (96 of 5554 genes) were more than two-fold differentially expressed following farnesol treatment. Conclusions:
2019-10-11 | GSE138731 | GEO
Project description:5mL PAO1 culture was mixed with PaoP5(dap1 mutant) or PaoP5 (MOI=10) for 10 min, and 5mL PAO1(lon mutant) was infected with aoP5(dap1 mutant) (MOI=10) for 10 min. The 1ml sample was then made into pellets. proteomic analysis was performed by Applied Protein Technologies. Biological replication tests were performed 3 times in each group. The samples were lysed with SDT buffer and quantified with BCA protein assay kit. The protein is digested with trypsin and then desalted with a C18 cartridge. The digested peptides were concentrated by vacuum centrifuge, recombined with formic acid, and then analyzed by LC-MS/MS. The peptides were uploaded to a reversed-phase column and connected to a C18 reversed-phase analysis column of formic acid, separated by a linear gradient buffer containing acetonitrile and formic acid at a flow rate of 300 nL/min. The mass spectrometer operates in positive ion mode. The original MS data of each sample were combined, and MaxQuant 1.5.3.17 software was used for identification and quant
2023-10-16 | PXD046148 |
Project description:Experimental Design Type of experiment: In order to evaluate the influence of subinhibitory concentrations of the macrolide antibiotic Azithromycin (AZM) on the global Pseudomonas aeruginosa gene expression, we performed a comparative gene expression analysis of AZM-treated versus untreated P. aeruginosa PAO1 cultures. Experimental factors: P. aeruginosa PAO1 cultures with and without addition of 2 µg/ ml AZM were grown until early stationary phase. Total RNA was extracted when the cultures reached an OD600 of 2.8. The transcriptomes of the untreated cultures were taken as reference values. Both of the AFFYMETRIX Chips of AZM-treated PAO1 (GSM45590, GSM45591) were compared with each of the two chips of the untreated PAO1 (GSM45588, GSM45589). Hybridization procedures and parameters: Hybridization of the probes was carried out according to the manufacturer’s “Expression Analysis Protocol (p. 25: Modified Fluidic Protocol for P. aeruginosa cDNA Assay)”, see http://www.affymetrix.com: Hybridization for 16 h at 50°C and 60 rpm. - Post Hyb Wash 1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C - Post Hyb Wash 2: 4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C - Stain: Stain the probe array for 10 minutes in Streptavidin Solution Mix at 25°C - Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 30°C - 2nd Stain Wash: Stain the probe array for 10 minutes in antibody solution at 25°C - 3rd Stain Wash: Stain the probe array for 10 minutes in SAPE solution at 25°C - Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Measurement of data and specifications: Data transformation and selection procedures: · The entire signals were scaled to 150 (4% capped median); scaling factors of the arrays were within 3.4 fold of each other, as the % genes called present were in the range of 23.7% and 38.1% for three arrays (GSM455889, GSM45589, GSM45591) and 74,4% for one array (GSM45590). The background levels (Average Background) were similar for all arrays (in a range of 47.20 and 55.64). The Q scores were comparable (in a range of 2.38 and 2.81). The Average Signals of the four arrays were similar (between 187.8 and 228.7). · Scanning hardware: AFFYMETRIX Scanner; software: AFFYMETRIX MAS 5 (Statistical Algorithms Reference Guide, http://www.affymetrix.com/support/technical/technotes/statistical_reference_guide.pdf), MICRO DB 3 and DMT 3 · Image analysis software: AFFYMETRIX MAS 5 Data selection: · Threshold of Signal Log ratio: -1/1; change is I (increased), MI (marginally increased), D (decreased), MD (marginally decreased); change p-value >0.999 or <0.001; only genes that are present (Detection=P) in at least one of the compared chipsets. · Only following genes were considered: Minimal threshold of regulation ±2 fold; minimal change p-values of 0.999 and 0.001, respectively; minimal difference of signal intensities of 200. · The final gene expression data table used by the authors to make their conclusions after data selection and transformation will be published as supplementary data. Keywords: other
2006-05-10 | GSE2430 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of diallyl disulphide-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 108 CFU/mL. Then DDS was added, with its concentrations were 0 (as control, three biological repeats numbered A1, A2, and A3) and 0.64 mg/mL (three biological repeats numbered B1, B2, and B3) separately, both with a triplicate. All the six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours. The cells were then sampled and centrifuged from the three control groups and three DDS treatment groups, respectively. The cell precipitates in the control and DDS-treated groups were quickly separately frozen at -80 ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: The RNA sequencing results revealed that a large number of genes in P. aeruginosa PAO1 were differentially expressed after DDS treatment. More than three thousands of genes were differentially expressed, with either up regulated (1649 genes) or down regulated (1725 genes) more than two-fold. Conclusions:
2018-08-21 | GSE118801 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of DAS-treated and DAE-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Results: The transcriptome sequencing data of control, DAS-treated and DAE-treated groups were compared and analyzed in the form of the following: DAE vs DAS, control vs DAS, and control vs DAE. The details of the differentially expressed genes among the three groups showed that the amount of differential expressed genes between DAE-treated group and DAS-treated group was high (total 2195, up-regulated 1608, down-regulated 587). There were many differentially expressed genes in the PAO1 strain after DAS treatment (total 2771, up-regulated 1905, down-regulated 866), while the amount of differentially expressed genes after DAE treatment was relatively small (total 770, up-regulated 349, down-regulated 421).
2020-12-31 | GSE151292 | GEO
Project description:Micoarrays were used to obtain gene expression in mid-log phase PAO1::cprR(PA3077) with the treatment of 12ug/ml CP28 vs mid-log phase PAO1 with the treatment of 12ug/ml CP28
2012-12-05 | E-MTAB-1276 | biostudies-arrayexpress
Project description:Transcriptomic analysis of PAO1 and PAO1/pUCP18::msr(E) strain under azithromycin treatment
| PRJNA381842 | ENA
Project description:Protein complexome analysis of Pseudomonas aeruginosa PAO1 at OD 0.3 in LB media through 10-40% glycerol gradient fractionation in 21 samples.
2021-01-06 | PXD021359 | Pride
Project description:Pseudomonas aeruginosa PAO1 persister and normal cells were treated with and without Granulocyte Macrophage Colony-Stimulating Factor (GM-CSF) to understand the effect of GM-CSF on gene expression of PAO1. We used DNA microarrays to identify the down-regulated and up-regulated genes after GM-CSF treatment.
2014-11-25 | GSE63588 | GEO