Methods for interrelating 'omics data

Actions

Order Studies

Overview
Related items

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:

Help

Tree Split Graph

Export PNG

Click below to download a copy of the image

Download

Creators and Submitter

Creators

Not specified

Submitter

Olga Krebs

Activity

Views: 1681

Created: 10th Jun 2009 at 17:09

Last updated: 10th Nov 2011 at 17:14

Related items

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

Advanced People list for this Investigation with search and filtering

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

Advanced Programmes list for this Investigation with search and filtering

Dummy programme

No description specified

Projects: SysMO DB

Web page: Not specified

Advanced Projects list for this Investigation with search and filtering

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

Advanced Studies list for this Investigation with search and filtering

Metabolomics data capture

SysMO DB

All creators

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

Advanced Assays list for this Investigation with search and filtering

Excel template for metabolomics data

SysMO DB

All creators

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

All creators

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

Advanced Data files list for this Investigation with search and filtering

5mM GLC runout data.

SysMO DB

All creators

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

Download

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

Treatments Test 1

SysMO DB

All creators

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

Download

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

Quyen data

SysMO DB

All creators

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

Download

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

Excell sheet template : concentrations of intracellular metabolites

SysMO DB

All creators

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

All creators

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

Download

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

test plot data

SysMO DB

All creators

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

Download

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

Umlaut only in cells

SysMO DB

All creators

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

All creators

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

Advanced Models list for this Investigation with search and filtering

Kinetic model for incubation

SysMO DB

All creators

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

Download

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

Advanced SOPs list for this Investigation with search and filtering

Validation experiments

SysMO DB

All creators

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

Download

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

new sop

SysMO DB

All creators

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

Download

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

Quyen's sop

SysMO DB

All creators

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

Download

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

Advanced Publications list for this Investigation with search and filtering

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