Data files

SAP4, SAP155, SAP185, SAP190, NHA1, SIT4

Creator: Silvia Petrezselyova

Contributor: The JERM Harvester

Data sheet generated in Greifswald to measure the response of sigB activity in response to different media composition.

Creator: Ulf Liebal

Contributor: Ulf Liebal

No description specified

Creator: Praveen Kumar Sappa

Contributor: The JERM Harvester

No description specified

Creators: Alexander Ter Beek, Klaas Hellingwerf

Contributor: The JERM Harvester

This is the csv version of the file: 091016 quinones complete data magdeburg

This document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.

Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried
...

his document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.

Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried out in Infors-Bioreactors at 0, 20, 50, 80, 100 and 120% aerobiosis. All data
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1_0

Creator: Dani Valverde

Contributor: The JERM Harvester

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

Contributor: The JERM Harvester

Strain BSA115 is grown until appr. OD 0.25 then expression of sigB is induced by the addition of IPTG. The extend of stress response is measured by the expression of lacZ via beta-Gal assay. The experiment lasts for appr. 400 min.

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Creator: Jost Ludwig

Contributor: The JERM Harvester

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

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Creator: Jost Ludwig

Contributor: The JERM Harvester

This Excel template is for use with affy transcriptomics data in Matrix table format. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

Output of the 3D-structures modeled by comparative modeling tool for LDH enzymes from four LABs (in the PDB format, tarred). Four LABs include Enterococcus faecalis, Lactococcus lactis, Streptococcus pyogenes and Lactobacillus plantarum. Output of the SEEK Model https://seek.sysmo-db.org/models/118.

The modeling was performed against a x-ray structure of LDH from B. stearothermophilis (template, PDH ID: 1LDN).

No description specified

Creator: Tomas Fiedler

Contributor: The JERM Harvester

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells exposed to methylene blue

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells under high pH stress (pH8.7)

Intracellular concentrations of 50 metabolites measured by LC-MS using isotope ratio based mass spectrometry technique

The Table represents the simulation results of how the presence of phosphate ions (Pi) in the solution might affect the activity of four LDH enzymes. This includes the algorithmic analysis of the binding energies values computed by the GRID program (see Part 4, model) for each enzyme in presence and absence of FBP molecule at pH 6 and 7. The analysis was performed by using the algorithm proposed in Part 5, model.

TbTryS activity was measured at 37°C in the in vivo-like buffer. All substrate stock solutions were prepared in the in vivo-like buffer and the pH was adjusted to 7.0. The assays were performed in a final volume of 2 ml and contained 0.2 mM NADH, 1 mM phosphoenolpyruvate, 4 units pyruvate kinase, 4 units L-lactate dehydrogenase, 0.17 µM TbTryS, 2.1 mM ATP and varying amounts of GSH, and Spd.

The file contains the initial rate measurements of TbTryS obtained under different substrate and product initial concentrations.

Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.

Creators: None

Contributor: Olga Krebs

No description specified

Creator: Margrete Solheim

Contributor: Margrete Solheim

No description specified

Creators: John Raedts, Wouter Kuit

Contributor: John Raedts

S. pneumoniae Control1 DNA-Seq PE1

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae Control 1 DNA PE2

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae Control 2 DNA PE1

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae Control 2 DNA PE2

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae HPUra 1 DNA PE1

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae HPUra 1 DNA PE2

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae HPUra 2 DNA PE1

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae HPUra 2 DNA PE2

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae kanamycin DNA PE1

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae kanamycin DNA PE2

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

E. coli DNA-Seq
Barcodes:
control 1: GTGGCC
control 2: GTTTCG
Trimethoprim 1: CACTCA
Trimethoprim 2: CAGGCG

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

E. coli RNA-Seq
Barcodes:
Control 1: AGTTCC
Control 2: ATGTCA

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

E. coli RNA-Seq
Barcodes:
Trimethoprim 1: CCGTCC
Trimethoprim 2: GTAGAG

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae RNA-Seq
Barcodes:
Control 1: CAGATC
Control 2: ACTTGA

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

S. pneumoniae RNA-Seq
Barcodes:
HPUra 1: CAGATC
HPUra 2: ACTTGA
Kanamycin: AGTCAA

Creator: Jan-Willem Veening

Contributor: Jan-Willem Veening

This document shows the ArcA phosphorylation levels at different aerobiosis units, measured using Phos-tag gels, western immunoblotting. Exposed films were quantitated using ImageJ and the results shown here.

Creator: Matthew Rolfe

Contributor: Matthew Rolfe

No description specified

Creator: Maike Bartholomae

Contributor: Maike Bartholomae

The pdf-file shows simulations of a hypothetical model of sigma factor competition. It simulates the dynamics that we can expect from the experiments and prepares for the analysis of the experimental data.
Analysis of sigma factor competition is based on a Lineweaver-Burk representation of RNApolymerase and competing sigma factors.

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell titers for every sample.

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell sizes for every sample.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl and glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl, without glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

BCN-RNAsample001

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample002

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample003

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample004

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample005

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample006

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample007

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample008

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample009

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample010

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample011

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample012

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample013

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample014

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample015

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample016

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample017

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample018

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample019

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample020

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample021

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample022

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample023

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample024

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample025

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample026

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample027

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample028

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample029

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample030

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample031

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample032

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample033

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample034

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample035

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

BCN-RNAsample036

Creator: Lina Patricia Barreto Parra

Contributor: The JERM Harvester

No description specified

batch fermatation - The transition from growing to non-growing Bacillus subtilis cells

Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

qATP values were calculated based on fermentation product formation and expected used biochemical pathways. These were averaged and used for calculation of the ATP required for maintenance and for growth. These data were subsequently used to calculate the qATP at the maximal growth rate by extrapolation

Creator: Martijn Bekker

Contributor: Martijn Bekker

No description specified

Creator: Joerg Stuelke

Contributor: Leif Steil

Table describing the catabolite repression of β-xylosidase by different carbon sources(glucose, sorbitol, fructose, maltose, glycerol. mannitol) in various mutants of CcpA cofactors (HprK, crh)

Creator: Joerg Stuelke

Contributor: Leif Steil

Cell volume_trk_

Creator: Silvia Petrezselyova

Contributor: The JERM Harvester

Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

S. pyogenes was grown in C-limited cultures at pH 6.5 and 7.5 and at a growth rate of 0.05
The glnA mutant strain shows decreased growth in low glutamine and excess glutamate conditions and no growth at all in low glutamine and low glutamate conditions. Preliminary results of glucose-limited chemostat cultures indicate a reversion of the pH dependency of the shift from homolactic to more mixed acid fermentation:
wild type - lactate/formate ratio at pH 6.5 = 11.8, at pH 7.5 = 2.8
glnA mutant -
...

E. faecalis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

L. lactis was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05, 0.15 and 0.40

S. pyogenes was grown in C-limited cultures at pH 6.7 and 7.5 and at a growth rate of 0.05 and 0.15

Measurements on Km, Vmax and allosteric activation or inhibition of the main L-lactate dehydrogenase

Creator: Tomas Fiedler

Contributor: Martijn Bekker

acetic acid puls during acidogenesis
shift to solventogensis
back-shift to acidogenesis
butyric acid puls during acidogenesis

butyric acid pulse during acidogenesis
acetic acid pulse during acidogenesis
butyric acid pulse during solventogenesis

This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model).
Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

Photos of drop test conpresed in .zip file

Creator: Jaromir Zahrádka

Contributor: The JERM Harvester

nha1, ena1-5, double deletion

Creator: Jaromir Zahrádka

Contributor: The JERM Harvester

The output includes the similarity matrix of LDH enzymes based on comparison of the electrostatic potentials at allosteric and catalytic binding sites, separately. The similarity indices were generated by the PIPSA program (http://projects.villa-bosch.de/mcmsoft/pipsa/3.0/).

L. lactis was grown in rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

Concentrations of 22 extracellular metabolites (major medium components) from T. b. brucei 427

Arginine kinase has been thought of as a potential stress marker (see 'Metabolic changes by oxidative stress in T. b. brucei 427'), the gene knockout cells have been constructed.

Creators: Dong-Hyun Kim, Eduard Kerkhoven

Contributor: Dong-Hyun Kim

In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.

Creator: Araz Zeyniyev

Contributor: Araz Zeyniyev

No description specified

Data for three biological replicates of control culture and 37°C and 57°C in the file.

B. subtilis was grown in M9 media with glucose as carbon source and the samples for RNA were harvested at OD600nm- 0.4 , 1.3 and 1.0 ). Culture was done at 37°C and samples at OD600nm- 0.4(Exponential), OD600nm- 1.3 (Early stationary), OD600nm-1.0(Late Stationary). All the samples were analysed for transcriptome as biological triplicates.

- automated integration of transcriptomic and reactome data to differential equations
- structure of the paths is maintained
- continuous fermentation model in standard format for data integration, two component model (cell and fermenter)

call >> Kegg2SBToolbox2('model_map.txt', 'reactions_compounds_final.csv','extracellular.txt','testmodel.txt') for an example

where
model_map is the desired mapping of species,
reaction_compounds_final.csv is the entire network,
extracellular.txt is a manual
...

WT (Cy5) vs. trxB (Cy3)_stationary growth phase_DyeFlip

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

WT (Cy3) vs. trxB (Cy5)_stationary growth phase

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

WT (Cy3) vs. trxB (Cy5)_exp. growth phase

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

E. faecalis was gucose-pulsed after resuspension in 100 mM MES buffer at pH 6.5
Intra- and extracellular metabolites concentrations were followed in time

Creator: Martijn Bekker

Contributor: Martijn Bekker

NHA1 ENA1-5 TOK1 TRK1 TRK2

Creator: Silvia Petrezselyova

Contributor: The JERM Harvester

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.

Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines,
...

Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.

Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR

by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels

TRK1, TRK2, NHA1, ENA1-5

Creator: Jaromir Zahrádka

Contributor: The JERM Harvester

TRK1, TRK2, TOK1, NHA1, ENA1-5

Creator: Jaromir Zahrádka

Contributor: The JERM Harvester

No description specified

Creator: Tomas Fiedler

Contributor: The JERM Harvester

For each modeled 3D structure of LHD (see Part 1: 3D structure modeling for LDH enzymes) was computed electrostatic potential by using the UHBD program. The files are in GRD format (binary) and can be visualized with the graphical programs as CHIMERA or VMD.

Monitoring of end products ethanol, acetone, butanol, acetate and butyrate during master fermentation of Clostridium acetobutylicum at the steady state pH values 5.5, 5.3, 5.1, 4.9 and 4.7.

Monitoring of end products in mM of ethanol, acetone, butanol, acetate and butyrate during master fermentation of Clostridium acetobutylicum at the steady state pH values 5.7 (acidogenesis) and 4.5 (solventogenesis).

This .csv file contains the entire transcriptional dataset of the aerobic to anaerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

This .csv file contains the entire transcriptional dataset of the anaerobic to aerobic transition. The values shown are the gene-expression ratio at 2, 5, 10, 15 and 20 minutes relative to the 0 minute timepoint.

No description specified

transcriptome, glucose, biomass data inside

Output files of phosphate probe binding on the surface of LDH from lactococcus lactis type 1. File with extension XPLOR can be visualized with a program VMD to identify the most favorable position for the phosphate binding. This relates to the Model "Part 4".

Excel sheet template : concentrations of intracellular metabolites

Experimental data for 3PG conversion to fructose-6-phosphase in reconstituted systems of gluconeogenesis of S. solfataricus

No description specified

Kinetic characterisation of FBPAase. Expermental data for enzyme reaction rates with increasing concentrations of DHAP and GAP.

Simulation results of FBPAase of experimental data for DHAP and GAP saturation

This .csv file shows FNR activity at different aerobiosis levels

Columns
a_old Desired aerobiosis level (Aerobiosis units or %AAU)
Bgal_activity Average FNR reporter activity (Miller units)
Bgal_STDEV STDEV of FNR reporter activities (Miller units)
rDOT(μM) Dissolved oxygen tension (μM)
DCW DCW (g/L)
[acetate] Extracellular acetate concentration (mM)
Qacetate Acetate flux (mmoles/h/gDCW)
a_new Actual aerobiosis level in sampled chemostat

A .pdf files showing graphs of FNR activity at varying aerobiosis levels

Top graph shows no acetate re-calibration
Bottom graph shows data with acetate re-calibration

pulse acetic acid: 70mM (2x), 80mM,
shift to 4.5,
pulse acetic acid: 70mM

acetic acid addition

step experiment:
50mM, 70mM, 100mM, 120mM

pulse
200mM

This .csv file contains the filtered datset of the anaerobic to aerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p

This .csv file contains the filtered datset of the aerobic to anaerobic transition. Values are shown if they show a statistically significant change relative to the 0 minute transcriptional profile (t-test p

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Kinetic characterisation of GAPDH. Expermental data for enzyme reaction rates with increasing concentrations of BPG, NADPH, NADP, GAP and Pi.

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

GCN4

Creator: Paul Heusden

Contributor: The JERM Harvester

This data file shows results from the different chemostat experiments.Gene expression rates are presented.

This template is for recording genome data from the NimbleGen platform.
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

Glucose pulsed L. lactis with 20 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

L. lactis was grown in LAB medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

Glucose pulsed S pyogenes with 5 mM glucose in 100 mM MES buffer at pH 6.5 and followed intracellular metabolites in time

No description specified

Creator: Margrete Solheim

Contributor: Margrete Solheim

No description specified

Creator: Margrete Solheim

Contributor: Margrete Solheim

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under aerobic batch conditions with glucose as substrate.

Measurement of by-product formation rates, substrate consumption rates and extracellular concentrations of cAMP under anaerobic batch conditions with glucose as substrate.

L. lactis cultures were grown at different dilution rates in glucose-limited chemostat conditions and were analyzed with respect to physiological parameters. Amino acid consumption, glucose consumption and production of fermentation products were measured in steady-state conditions,

Creator: Martijn Bekker

Contributor: Martijn Bekker

The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA
...

In Bacillus subtilis and its relatives carbon catabolite control, a mechanism enabling to reach maximal efficiency of carbon and energy sources metabolism, is achieved by the global regulator CcpA (carbon catabolite protein A). CcpA in a complex with HPr-Ser-P (seryl-phosphorylated form of histidine-containing protein, HPr) binds to operator sites called catabolite responsive elements, cre. Depending on the cre box position relative to the promoter, the CcpA/HPr-Ser-P complex can either act as a
...

Creator: Oscar Kuipers

Contributor: Leif Steil

Describes the assumptions made, how to integrate the new reactions to the rest of the glycolysis model, the parameters needed and the preliminary parameter values collected from the litterature.

Creator: Fiona Achcar

Contributor: Fiona Achcar

call
ConvertStdModel2SBTtest('Conti_Ferm_Std', 'CD_Transcriptomic.csv', 'glucose.csv', 'OD.csv',0)

Some home work for PALs to prepare Lightning Talks and ISBE/ESFRI Sessions

Creator: Olga Krebs

Contributor: Olga Krebs

In this experiment we glucose-pulsed an L. lactiss cultures re-suspended in 100 mM MES buffer at pH 6.5. Samples were taken in time to study intra- and extracellular metabolites. These data are used to construct a kinetic model of the catabolism of E. L. lactis

Lactobacillus plantarum ATCC 14917 differentially expressed proteins, comparison between low and high growth rates

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum strains WCFS1, NC8, ATCC14917, JDM1. HPLC end products mM measurements (CDM subtracted) and flux calculations, high and low growth rates.

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum JDM1 differentially expressed proteins, comparison between low and high growth rates

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum NC8 differentially expressed proteins, comparison between low and high growth rates

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum WCFS1 differentially expressed proteins, comparison between low and high growth rates

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum strains WCFS1, NC8, JDM1 and ATCC 14917 amino acid concentrations mM supernatant, high (D=0.4) and low (D=0.05) growth rates

Creator: Anette McLeod

Contributor: Anette McLeod

Lactobacillus plantarum, 4 strains (WCFS1, NC8, ATCC 14917, JDM1) chemostat experiments low and high growth rates, OD and DW measurements

Creator: Anette McLeod

Contributor: Anette McLeod

Confocal microscopy of Arl1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Creator: Paul Heusden

Contributor: Paul Heusden

Confocal microscopy of CIN5-GFP from the collection of GFP strains at standard growth conditions (50 mM KCl)

Creator: Paul Heusden

Contributor: Paul Heusden

Confocal microscopy of Ena1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Creator: Paul Heusden

Contributor: Paul Heusden

Confocal microscopy of HOG1-GFP from GFP-strain collection under standard growth cionditions (50 mM KCl).

Creator: Paul Heusden

Contributor: Paul Heusden

Confocal microscopy of Nha1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Creator: Paul Heusden

Contributor: Paul Heusden

Confocal microscopy of Pma1-GFP cells after 60 min at 0 or 50 mM KCl .

Creator: Paul Heusden

Contributor: Paul Heusden

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_0

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_10

Creator: Dani Valverde

Contributor: The JERM Harvester

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_20

Creator: Dani Valverde

Contributor: The JERM Harvester

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_40

Creator: Dani Valverde

Contributor: The JERM Harvester

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_5

Creator: Dani Valverde

Contributor: The JERM Harvester

Growth yeast with 50mM K+ and long timing collection

Creator: Dani Valverde

Contributor: The JERM Harvester

MS001_60

Creator: Dani Valverde

Contributor: The JERM Harvester