Dataset Information

MStern Blot - Urinary Biomarker Study

ABSTRACT: This large-scale study focused on the discovery on urinary biomarker for ovarian cyst.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Urine

DISEASE(S): Ovarian Cyst

SUBMITTER: Sebastian Berger

LAB HEAD: Hanno Steen, PhD

PROVIDER: PXD002549 | Pride | 2015-07-30

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	141121_JM_Thermo-DIA_MStern-plate1_75min_DDA_4ul_A01.raw	Raw
	141121_JM_Thermo-DIA_MStern-plate1_75min_DDA_4ul_A02.raw	Raw
	141121_JM_Thermo-DIA_MStern-plate1_75min_DDA_4ul_A03.raw	Raw
	141121_JM_Thermo-DIA_MStern-plate1_75min_DDA_4ul_A04.raw	Raw
	141121_JM_Thermo-DIA_MStern-plate1_75min_DDA_4ul_A05.raw	Raw

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Publications

MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates.

Berger Sebastian T ST Ahmed Saima S Muntel Jan J Cuevas Polo Nerea N Bachur Richard R Kentsis Alex A Steen Judith J Steen Hanno H

Molecular & cellular proteomics : MCP 20150729 10

We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membra ...[more]

PMID: 26223766

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Project description:Pseudomonas aeruginosa is one of the most frequent pathogen dominant in complicated urinary tract infections (UTI). To unravel the adaptation strategies of P. aeruginosa to the conditions in the urinary tract and to define the underlying regulatory network an artificial growth system mimicking the conditions in the urinary tract was established. Transcriptome analyses were used to investigate the physiological status of P. aeruginosa under this conditions. We performed comparisons to identify genes induced under artificial urinary tract conditions to unravel the adaptive strategies and the underlying regulatory network used by Pseudomonas aeruginosa during urinary tract infections using Affimetrix GeneChips. Pseudomonas aeruginosa wild type strain PAO1 was grown in an artificial in vitro growth system mimicking the conditions in the urinary tract. Therefore, biofilms were grown on the surface of membrane filters placed on agar plates at 37 Â°C up to the late logarithmic state under aerobic and anaerobic conditions (incubated in an anaerobic beanch). An artificial urine medium (AUM) simulating the averaged urine of an human adult was used as nutrient souce. 10-fold diluted Luria Bertani (LB)-medium was used as reference medium. For growth under oxygen depletion the media were supplemented with 50 mM KNO3 to sustain anaerobic respiration. The biofilms were harveted at this time points and resuspsended in 0.9% (w/v) NaCl. The OD578 of biofilm suspension was 0.8 for all tested conditions. First comparison: Identification of genes induced or repressed under aerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown aerobically for 18 h to the late logarithmic phase in biofilms on AUM with the transcriptome profile of the PAO1 strain, which was grown aerobically for 18 h to the late logarithmic phase in biofilms on 10-fold diluted LB. Second comparison: Identification of genes induced or repressed under anaerobic conditions in the P. aeruginosa wild type PAO1. Here we compared the transcriptome profile of P. aeruginosa PAO1 grown anaerobically for 2 days up to the late logarithmic phase in biofilms on AUM supplemented with 50 mM nitrate with the transcriptome profile of the PAO1 strain, which was grown anaerobically for 2 days up to the late logarithmic phase in biofilms on 10-fold diluted LB supplemented with 50 mM nitrate.