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M9_shake_flask_exp_trans_stat_transcriptome_nimblegen

BaCell-SysMO

No description specified

Creator: Praveen kumar Sappa

Submitter: Praveen kumar Sappa

Investigations: Redefining the Complete Transcriptome of Bacill...

Studies: Transcriptome analysis of glucose starvation in...

Assays: Tiling Array analysis of glucose strarved B. su...

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Created: 30th Mar 2012 at 11:37, Last updated: 30th Apr 2012 at 13:03

Map with simulation results

SUMO

The abscissa of the plots shows the percentage of aerobiosis that is a physiological measure for oxygen availability (http://www.ncbi.nlm.nih.gov/pubmed/11844770).

Grey Boxes: Enzymes & Reactions blue lines/symbols: flux in mmol per gramm dry cell weight an hour red lines/symbols: mRNA levels
White Boxes: Intracellular and extracellular metabolites blue lines/symbols: concentration of the metabolites (extracellular: mM, intracellular: AU)
Yellow Boxes: Aggregated Quantities as yield, ...

Creator: Michael Ederer

Submitter: Michael Ederer

Investigations: Steady state studies for different oxygen avail...

Studies: The Escherichia coli steady state response to o...

Assays: Steady State Oxygen Response of E. coli WT and ...

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Created: 19th Dec 2012 at 15:02, Last updated: 19th Dec 2012 at 15:10

Maximal specific growth rates of the three lactic acid bacteria and their ldh deletions.

SysMO-LAB

. L. lactis (NZ9000), E. faecalis (V538) and S. pyogenes (M49) wild type strain and their ldh- mutants were grown in batch cultures at 37°C in anaerobic 96 wells plates in either TH-broth supplemented with 0.5% (w/v) yeast (THY) or a chemically defined medium for LAB (pH 7.4) (CDM-LAB (10)). Both media were buffered with either 100 mM MES buffer or 100 mM MOPS buffer for growth at pH 6.5 and 7.5 respectively.

Creators: Martijn Bekker, Tomas Fiedler

Submitter: Martijn Bekker

Investigations: Investigation of glycolysis and pyruvate branch...

Studies: Study of the physiological characterization of ...

Assays: Maximal specific growth rates of the three lact...

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Created: 28th Jul 2011 at 11:31, Last updated: 11th May 2016 at 15:19

Measured steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat

MOSES

Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(R) except CO2, which is in parts of the partial pressure.

Creator: Maksim Zakhartsev

Submitter: Maksim Zakhartsev

Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...

Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y...

Assays: MOSES: dynamic model of glucose pulse, Steady state concentrations of extracellular me...

Created: 27th Apr 2010 at 09:26, Last updated: 30th Jan 2012 at 09:49

Measured steady state concentrations of intracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat

MOSES

Steady state concentrations of intracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(CV).

Creator: Maksim Zakhartsev

Submitter: Maksim Zakhartsev

Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...

Studies: Metabolic perturbation of the steady state cult..., Steady state concentrations of metabolites in y...

Assays: MOSES: dynamic model of glucose pulse, Steady state concentrations of intracellular me...

Created: 27th Apr 2010 at 09:42, Last updated: 30th Jan 2012 at 09:51

Measured steady state metabolic fluxes

MOSES

Steady state metabolic fluxes measured in glucose-limited chemostat of Saccharomyces cerevisiae at D = 0.1 h-1 growing on minimal medium. Fluxes are: glucose, ethanol, glycerol, acetate, succinate, pyruvate, lactate, citrate, malate, a-ketoglutarate, fumarate

Creator: Maksim Zakhartsev

Submitter: Maksim Zakhartsev

Investigations: Kinetic analysis of metabolic system using tran..., Steady state metabolic fluxes and metabolite co...

Studies: Metabolic perturbation of the steady state cult..., Steady state fluxes in yeast Saccharomyces cere...

Assays: MOSES: dynamic model of glucose pulse, Steady state extracellular fluxes in anaerobic ...

Created: 27th Apr 2010 at 08:30, Last updated: 30th Jan 2012 at 09:47

Measurement of intracellular K+ content of cells lacking TRK1 an

TRANSLUCENT

No description specified

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 1st Jun 2010 at 18:20, Last updated: 1st Jun 2010 at 18:20

Measurements on kinetics of L-LDHs from different latic acid bacteria at pH 6.0 and pH 7.0.

SysMO-LAB

Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model .

Creators: None

Submitter: Silvio Hering

Investigations: Investigation of glycolysis and pyruvate branch...

Studies: Comparative modeling and phosphate dependence f...

Assays: Regulation of the activity of lactate dehydroge...

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Created: 2nd Apr 2012 at 14:22, Last updated: 19th May 2014 at 13:24

Measurements on kinetics of L-LDHs from L.lactis at pH 7.5

SysMO-LAB

Heterologous Expression of LDH from L.actis (MG1363) in E. coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model

Creator: Wayne Aubrey

Submitter: Wayne Aubrey

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 30th Jan 2013 at 10:36, Last updated: 12th May 2016 at 14:25

Meeting location map

SysMO DB

Meeting location map

Creator: Olga Krebs

Submitter: Olga Krebs

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 16th Sep 2013 at 14:48

Mem. potential o

TRANSLUCENT

none

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 4th Jun 2010 at 16:31, Last updated: 4th Jun 2010 at 16:31

Membrane potenti

TRANSLUCENT

TRK1, TRK2

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 4th Jun 2010 at 15:56

Membrane potenti

TRANSLUCENT

AFG3, AKR1, BRP1, COG6, ERG6, HRK1, LST7, NHX1, PEP5, PIG1, PTK2, RCK2, RCY1, REF2, RIC1, RTS1, SGF11, SAP185, SKY1, SNC2, SUR2,

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 4th Jun 2010 at 16:20

Metabolic changes by oxidative stress in T. b. brucei 427

SilicoTryp

Untargeted and targeted metabolic analysis on T. b. brucei 427 grown under oxidative stress with methylene blue has been carried out. This work has been completed with 11 bio-reps and found significant metabolic changes as you can see in the IDEOM file attached. 'Comparison' tab in the data spread sheet shows heat maps and fold change analysis regarding different metabolite levels (T: T brucei, TMB: T. brucei exposed to methylene blue, numbers: time points, 0, 5, 60 & 120min). If you double ...

Creator: Dong-Hyun Kim

Submitter: Dong-Hyun Kim

Investigations: Metabolite profiling, quantification and flux q...

Studies: Untargeted metabolite analysis

Assays: Metabolite profiling on T. brucei exposed to ox...

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Created: 26th Apr 2012 at 14:22, Last updated: 11th Jan 2013 at 16:15

Metabolite data from Vmax sampling of E. faecalis at three different dilution rates by enzymatic kits

SysMO-LAB

No description specified

Creator: Margrete Solheim

Submitter: Margrete Solheim

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 30th Nov 2012 at 09:38, Last updated: 12th May 2016 at 14:25

Metabolite data from Vmax sampling of E. faecalis at three different dilution rates by HPLC and GC

SysMO-LAB

No description specified

Creator: Margrete Solheim

Submitter: Margrete Solheim

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 30th Nov 2012 at 09:40, Last updated: 12th May 2016 at 14:25

Metabolome Data

BaCell-SysMO

SysMo2: Intra- and extracellular metabolome data of the chemostat experiments: nitrogen limitation, nitrogen limitation+ NaCl, nitrogen limitation + glucose

Creator: Hanna Meyer

Submitter: Hanna Meyer

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

Created: 30th Dec 2013 at 16:33, Last updated: 20th May 2014 at 14:53

Metabolomics Master Excel Template

SysMO DB

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

Creators: Katy Wolstencroft, Olga Krebs

Submitter: Katy Wolstencroft

Investigations: Creating data sheet template for 'omics data

Studies: Creating template for metabolomics data

Assays: Metabolomics Master Template

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Created: 28th Feb 2012 at 15:09, Last updated: 12th Feb 2020 at 08:42

Metall Stress

TRANSLUCENT

Metall Stress

Creator: Susanne Gerber

Submitter: The JERM Harvester

Investigations: No Investigations

Studies: No Studies

Assays: No Assays

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Created: 4th Jun 2010 at 16:08, Last updated: 4th Jun 2010 at 16:08

MK453

Noisy-Strep

No description specified

Creator: Jan-Willem Veening

Submitter: Jan-Willem Veening

Investigations: Chromosome segregation and cell division in Str...

Studies: Genome wide marker frequency analysis on new st...

Assays: Whole genome sequencing (Illumina)

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Created: 5th Aug 2016 at 14:47

MK454

Noisy-Strep

No description specified

Creator: Jan-Willem Veening

Submitter: Jan-Willem Veening

Investigations: Chromosome segregation and cell division in Str...

Studies: Genome wide marker frequency analysis on new st...

Assays: Whole genome sequencing (Illumina)

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Created: 5th Aug 2016 at 14:51

Model-representations-BSA115-Experiments

BaCell-SysMO

The figure contains information necessary to understand the mathematical model of experiments in BSA115. In these experiments sigB response is artificially initiated by the addition of IPTG while sigB is downstream of a Pspac promoter. The figure shows a flow-chart diagram that combines three hypotheses to explain experiments. It contains the ODEs and the fit of the respective models to the data.

Creator: Ulf Liebal

Submitter: Ulf Liebal

Investigations: The transition from growing to non-growing Baci...

Studies: Controlled sigmaB induction in shake flask

Assays: IPTG induction of sigmaB in BSA115

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Created: 2nd Feb 2011 at 16:42, Last updated: 2nd May 2012 at 11:49

mRNA decay

SilicoTryp

No description specified

Creator: Abeer Fadda

Submitter: Abeer Fadda

Investigations: Gene expression in Trypanosoma brucei

Studies: Determination and integration of abundance, pro...

Assays: Modelling the gene expression cascade with leng..., mRNA decay assay

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Created: 21st Mar 2012 at 19:01, Last updated: 20th Nov 2014 at 08:34

mRNA half-lives

SilicoTryp

This files contains the parameter values, life-times, half-lives and errors associated with modeling the decay of the transcriptome, based on 3 models described in Deneke et al. "Complex degradation processes lead to non-exponential decay patters and age-dependent decay rates of messenger RNA". PLoS One. 2013;8(2):e55442

Creator: Abeer Fadda

Submitter: Abeer Fadda

Investigations: Gene expression in Trypanosoma brucei

Studies: Determination and integration of abundance, pro...

Assays: Modelling the gene expression cascade with leng..., mRNA decay assay

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Created: 27th Jan 2014 at 17:54, Last updated: 20th Nov 2014 at 08:32

mRNAs with decreased abundance in RNaseY mutant

BaCell-SysMO