Methods for interrelating 'omics data

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This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.

SEEK ID: https://testing.sysmo-db.org/investigations/1

Projects: SysMO DB

Investigation position:

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Creators and Submitter

Creators

Not specified

Submitter

Olga Krebs

Activity

Views: 1767

Created: 10th Jun 2009 at 17:09

Last updated: 10th Nov 2011 at 17:14

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People (1)
Programmes (1)
Projects (1)
Studies (1+1)
Assays (2+1)
Data files (8)
Models (1)
SOPs (4)
Publications (1)

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Olga Krebs

Projects: SysMO DB, Xiaoming Test, Olga's test project, project created by programme admin Olga

Institutions: HITS gGmbH

Expertise: Genetics, Molecular Biology, Bioinformatics, Data Management, Transcriptomics

Tools: Databases, data modeling, ontology

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Dummy programme

No description specified

Projects: SysMO DB

Web page: Not specified

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SysMO DB

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

maximises the ‘shelf life’ and utility of data generated by SysMO;
provides an integrated platform for the dissemination ...

Programme: Dummy programme

Public web page: http://www.sysmo-db.org/

Organisms: Lactic Acid Bacteria, Agapornis

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Metabolomics data capture

SysMO DB

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Olga Krebs

No description specified

Submitter: Olga Krebs

Investigation: Methods for interrelating 'omics data

Assays: Excel template for metabolomics data, GLC incubation

Snapshots: No snapshots

Created: 10th Jun 2009 at 17:10, Last updated: 10th Nov 2011 at 17:14

1 hidden item

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Excel template for metabolomics data

SysMO DB

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Olga Krebs

Dear SEEK users, this Assay is just an example Excell sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat

Submitter: Olga Krebs

Assay type: Amplification

Technology type: Mass Spectrometry

Investigation: Methods for interrelating 'omics data

Study: Metabolomics data capture

Organisms: Callimico goeldii

SOPs: new sop

Data files: Excell sheet template : concentrations of intra..., Treatments Test 1, Umlaut in sheet names from Excel, Umlaut only in cells, a_transcriptome from BII-S-1, test plot data

Snapshots: No snapshots

Created: 10th Jun 2009 at 17:22, Last updated: 23rd Jun 2021 at 12:40

GLC incubation

SysMO DB

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Quyen Yamanaka

No description specified

Submitter: Quyen Yamanaka

Biological problem addressed: Metabolism

Investigation: Methods for interrelating 'omics data

Study: Metabolomics data capture

Organisms: Bacillus subtilis, Clostridium acetobutylicum, Bacillus subtilis : 168b (del ase / dasfadsf)

Models: Kinetic model for incubation

SOPs: Quyen's sop, Validation experiments, ^K blabla

Data files: 5mM GLC runout data., Quyen data

Snapshots: No snapshots

Created: 16th Nov 2015 at 16:49, Last updated: 26th Sep 2017 at 10:54

1 hidden item

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5mM GLC runout data.

SysMO DB

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Stuart Owen

No description specified

Creator: Stuart Owen

Submitter: Stuart Owen

Investigations: Glucose metabolism in Plasmodium falciparum tro..., Methods for interrelating 'omics data

Studies: Metabolomics data capture, Model validation

Assays: GLC incubation, GLC incubation

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Created: 10th Jul 2015 at 14:24, Last updated: 10th Jul 2015 at 14:29

Treatments Test 1

SysMO DB

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Stuart Owen

No description specified

Creator: Stuart Owen

Submitter: Stuart Owen

Investigations: Glycerol Synthesis in Saccharomyces cerevisiae, Methods for interrelating 'omics data

Studies: Metabolomics data capture and 1 hidden item

Assays: Excel template for metabolomics data, fffff

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Created: 15th May 2012 at 13:43, Last updated: 26th Jun 2015 at 10:27

Quyen data

SysMO DB

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Quyen Yamanaka

No description specified

Creator: Quyen Yamanaka

Submitter: Quyen Yamanaka

DOI: 10.5072/seek.datafile.80.2

Investigations: Growth control of the eukaryote cell: a systems..., Methods for interrelating 'omics data

Studies: Metabolomics data capture and 1 hidden item

Assays: GLC incubation, test assay

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Created: 11th Jun 2012 at 09:55, Last updated: 26th Jun 2015 at 10:27

Excell sheet template : concentrations of intracellular metabolites

SysMO DB

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Olga Krebs

Excell sheet template : concentrations of intracellular metabolites

Creator: Olga Krebs

Submitter: Olga Krebs

Investigations: Glycolitic Flux in Lactococcus lactis, Growth control of the eukaryote cell: a systems..., Methods for interrelating 'omics data

Studies: Metabolomics data capture, The effects of Redox Charge on Glycolytic Flux, test study

Assays: Excel template for metabolomics data, test for biol problem and 1 hidden item

Created: 10th Jun 2009 at 17:35, Last updated: 26th Jun 2015 at 10:27

a_transcriptome from BII-S-1

SysMO DB

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Katy Wolstencroft

Results of transcriptional profile in saccharomyces cerevisiae under different experimental conditions

Creator: Katy Wolstencroft

Submitter: Katy Wolstencroft

Investigations: Growth control of the eukaryote cell: a systems..., Methods for interrelating 'omics data, inv1

Studies: Metabolomics data capture and 2 hidden items

Assays: Changes in flux on the transcriptome, Excel template for metabolomics data and 1 hidden item

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Created: 16th Oct 2009 at 13:25, Last updated: 16th Apr 2013 at 10:09

test plot data

SysMO DB

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Stuart Owen

ttt

Creator: Stuart Owen

Submitter: Stuart Owen

Investigations: Methods for interrelating 'omics data, inv1 and 1 hidden item

Studies: Metabolomics data capture, study1, test quyen study

Assays: Excel template for metabolomics data, Testing assay for project browser thingy and 1 hidden item

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Created: 25th Aug 2011 at 16:33, Last updated: 5th Apr 2013 at 08:58

Umlaut only in cells

SysMO DB

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Stuart Owen

No description specified

Creator: Stuart Owen

Submitter: Stuart Owen

Investigations: Glycolitic Flux in Lactococcus lactis, Methods for interrelating 'omics data

Studies: Metabolomics data capture, The effects of Redox Charge on Glycolytic Flux

Assays: Excel template for metabolomics data and 1 hidden item

Created: 9th Mar 2012 at 09:34, Last updated: 9th Mar 2012 at 09:50

Umlaut in sheet names from Excel

SysMO DB

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Stuart Owen

No description specified

Creator: Stuart Owen

Submitter: Stuart Owen

Investigations: Methods for interrelating 'omics data

Studies: Metabolomics data capture

Assays: Excel template for metabolomics data

Created: 9th Mar 2012 at 09:29

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Kinetic model for incubation

SysMO DB

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Stuart Owen

Glycolytic model for Plasmodium falciparum; closed system

Creator: Stuart Owen

Submitter: Stuart Owen

Model type: Not specified

Model format: Not specified

Environment: Not specified

DOI: 10.5072/seek.model.98.1

Organism: Not specified

Investigations: Glucose metabolism in Plasmodium falciparum tro..., Methods for interrelating 'omics data

Studies: Metabolomics data capture, Model validation

Assays: GLC incubation, GLC incubation

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Created: 10th Jul 2015 at 14:23, Last updated: 10th Jul 2015 at 14:29

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Validation experiments

SysMO DB

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Stuart Owen

Finn Bacall

SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.

Creators: Stuart Owen, Finn Bacall

Submitter: Stuart Owen

Investigations: Glucose metabolism in Plasmodium falciparum tro..., Investigation with some private bits, Methods for interrelating 'omics data

Studies: Metabolomics data capture, Model validation, Public Study for OPSK-457

Assays: GLC incubation, GLC incubation, testing extraction title

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Created: 10th Jul 2015 at 14:22, Last updated: 2nd Mar 2017 at 14:18

new sop

SysMO DB

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Lihua Angel

No description specified

Creator: Lihua Angel

Submitter: queeny Nguyen

Investigations: Methods for interrelating 'omics data, inv1 and 1 hidden item

Studies: Metabolomics data capture and 2 hidden items

Assays: Excel template for metabolomics data, demo modelling analysis and 1 hidden item

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Created: 26th Jun 2012 at 13:01, Last updated: 16th Apr 2013 at 09:03

Quyen's sop

SysMO DB

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Quyen Yamanaka

edited to test subscription emails

Creators: None

Submitter: Quyen Yamanaka

Investigations: An example Investigation with Scale, Methods for interrelating 'omics data

Studies: Metabolomics data capture, a test study

Assays: Assay with a SOP, GLC incubation, Modelling Assay with a SOP

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Created: 11th Jun 2012 at 08:24, Last updated: 5th Apr 2013 at 09:02

^K blabla

SysMO DB

No description specified

Creators: None

Submitter: Deleted submitter

Investigations: Methods for interrelating 'omics data

Studies: Metabolomics data capture

Assays: GLC incubation

Created: 9th Mar 2012 at 14:27

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Phenomenon of hot-cold hemolysis: chelator-induced lysis of sphingomyelinase-treated erythrocytes

SysMO DB

Abstract (Expand)

Staphylococcus aureus produces a phospholipase C specific for sphingomyelin (beta-hemolysin). Erythrocytes with approximately 50% sphingomyelin in their membranes, e.g., from sheep, have been shown to … have up to 60% of this phospholipid hydrolyzed by this enzyme at 37 C in isotonic buffered saline without hemolysis. Cooling of sphingomyelinase C-treated erythrocytes to 4 C causes complete lysis of the cells, a phenomenon known as hot-cold hemolysis. The addition of ethylenediaminetetraacetate (EDTA) to sheep erythrocytes preincubated with sphingomyelinase C was found to induce rapid hemolysis at 37 C. The treated cells became susceptible to chelator-induced hemolysis and to hot-cold hemolysis simultaneously, and the degree of lysis of both mechanisms increased equally with prolonged preincubation with sphingomyelinase C. Erythrocytes of species not readily susceptible to hot-cold hemolysis were equally insusceptible to chelator-induced lysis. Chelators of the EDTA series were the most effective, whereas chelators more specific for Ca2+, Zn2+, Fe2+, Cu2+, and Mg2+ were without effect. The rate of chelator-induced lysis was dependent on the preincubation period with beta-hemolysin and on the concentration of chelator added. The optimal concentration of EDTA was found to equal the amount of exogenously added Mg2+, a cation necessary for sphingomyelinase C activity. Hypotonicity increased the rate of chelator-induced hemolysis, whereas increasing the osmotic pressure to twice isotonic completely inhibited chelator-induced lysis. The data suggest that exogenously added and/or membrane-bound divalent cations are important for the stability of sphingomyelin-depleted membranes. The phenomenon of hot-cold hemolysis may be a consequence of the temperature dependence of divalent ion stabilization.

Authors: C J Smyth, R Möllby, T Wadström

Date Published: 1st Nov 1975

Publication Type: Not specified

PubMed ID: 333

Citation:

Created: 21st Sep 2012 at 13:53, Last updated: 24th Mar 2022 at 10:39