Assays

What is an Assay?

8 Assays visible to you, out of a total of 11

RNA-Seq PA14 A549

Pseudomonas aeruginosa and its vesicles

Cells were seeded in 6-well plates and incubated at 37 °C and 5 % CO2 overnight. The next day, cells were washed with 1X PBS, treated with BMVs and incubated at 37 °C and 5 % CO2 for 24 h. RNA isolation was performed by using the NucleoSpin® RNA kit (MACHEREY-NAGEL, 740955.50). cDNA synthesis was performed and libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina at the Genome Analytics at Helmholtz Centre for Infection Research. Libraries were sequenced ...

Submitter: Meina Neumann-Schaal

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: 1 hidden item

Study: RNASeq comparing vesicle-treated to a non-treat...

Organisms: No organisms

SOPs: No SOPs

Data files: RNA-Seq PA14 A549

Snapshots: No snapshots

Created: 11th Aug 2025 at 06:02, Last updated: 12th Aug 2025 at 04:13

EbN1 Systems Biology

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No description specified

Submitter: Lars Wöhlbrand

Assay type: Protein Identification

Technology type: Liquid Chromatography-tandom Mass Spectrometry

Investigation: Systems biology investigation of aromatic compo...

Study: Experimental multi-OMICS

Organisms: No organisms

SOPs: SOP – Protein preparation, nanoLC-MS/MS analyse...

Data files: Detailed peptide data for identified proteins, Protein identification data

Snapshots: No snapshots

Created: 3rd Jun 2022 at 09:03, Last updated: 11th Apr 2024 at 08:15

GC-MS based analysis of metabolites

Adaptation of Salmonella enterica

No description specified

Submitter: Meina Neumann-Schaal

Assay type: Experimental Assay Type

Technology type: Gas Chromatography Mass Spectrometry

Investigation: Salmonella enterica relies on carbon metabolism...

Study: Metabolic analysis of Salmonella enterica to st...

Organisms: No organisms

SOPs: No SOPs

Data files: Salmonella enterica_metabolite data

Snapshots: Snapshot 1

Created: 21st Mar 2023 at 07:07, Last updated: 28th Aug 2023 at 13:57

EbN1 Systems Biology

No description specified

Submitter: Meina Neumann-Schaal

Assay type: Metabolite Profiling

Technology type: Liquid Chromatography Mass Spectrometry

Investigation: Systems biology investigation of aromatic compo...

Study: Experimental multi-OMICS

Organisms: Aromatoleum aromaticum

SOPs: SOP_analysis_CoA-esters, SOP_data_evalutation_CoA-esters, SOP_extraction_CoA-esters

Data files: CoA LC/MS Data Sample Identification, NO3_MS_CoA_Data, O2_MS_CoA_Data, Results - CoA-esters via LC-MS

Snapshots: No snapshots

Created: 20th Apr 2022 at 12:57, Last updated: 13th Oct 2022 at 13:56

non-volatile metabolites GC/MS

EbN1 Systems Biology

No description specified

Submitter: Sarah Kirstein

Assay type: Experimental Assay Type

Technology type: Gas Chromatography Mass Spectrometry

Investigation: Systems biology investigation of aromatic compo...

Study: Experimental multi-OMICS

Organisms: No organisms

SOPs: SOP - Analysis of non-volatile, small, polar me..., SOP - Data evaluation of non-volatile, small, p..., SOP - Extraction of non-volatile, small, polar ...

Data files: NO3_MS_small_metabolites_Data, Non-volatile, small, polar metabolites´GC/MS da..., O2_MS_small_metabolites_Data, Results - Non-volatile, small, polar metabolite...

Snapshots: No snapshots

Created: 25th Apr 2022 at 11:33, Last updated: 13th Oct 2022 at 13:54

Cultivation for multi-OMICS

EbN1 Systems Biology

Harvest optical densites and methods of transcriptom, proteom and metabolom samples for all tested substrat conditions.

Submitter: Meina Neumann-Schaal

Assay type: Experimental Assay Type

Technology type: Cultivation experiment

Investigation: Systems biology investigation of aromatic compo...

Study: Experimental multi-OMICS

Organisms: No organisms

SOPs: SOP – Substrate adaptation, cultivation and har...

Data files: No Data files

Snapshots: No snapshots

Created: 20th Apr 2022 at 13:02, Last updated: 13th Oct 2022 at 07:48

Metabolic modeling of EbN1

EbN1 Systems Biology

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All flux balance analyses of the stoichiometric model

Submitter: Julia Koblitz

Biological problem addressed: Modelling analysis

Investigation: Systems biology investigation of aromatic compo...

Study: Metabolic Modelling

Organisms: Aromatoleum aromaticum : EbN1T (wild-type / wild-type)

Models: EbN1 stoichiometric model iAA835 (Metano), EbN1 stoichiometric model iAA835 (SBML)

SOPs: No SOPs

Data files: Model | Biomass composition, Model | Flux balance analysis (FBA), Model | Simulation parameters and results

Snapshots: No snapshots

Created: 15th Jul 2022 at 06:32, Last updated: 13th Oct 2022 at 07:44

Scenario files for Metano metabolic modeling

EbN1 Systems Biology

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All files for metabolic modeling using the Metano toolbox, including the scenarios and flux balance analyses.

Submitter: Julia Koblitz

Biological problem addressed: Model Analysis Type

Investigation: Systems biology investigation of aromatic compo...

Study: Metabolic Modelling

Organisms: No organisms

Models: EbN1 stoichiometric model iAA835 (Metano)

SOPs: No SOPs

Data files: Model - Scenario - 3-HBz aerobic, Model - Scenario - 3-HBz anaerobic, Model - Scenario - 4HPP aerobic, Model - Scenario - 4HPP anaerobic, Model - Scenario - Acetate aerobic, Model - Scenario - Acetate anaerobic, Model - Scenario - Benzoate aerobic, Model - Scenario - Benzoate anaerobic, Model - Scenario - Phenylalanine aerobic, Model - Scenario - Phenylalanine anaerobic

Snapshots: No snapshots

Created: 15th Jul 2022 at 06:07, Last updated: 13th Oct 2022 at 07:43

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