Data files
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Experimental data set for the kinetic characterisation of PGK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Experimental data set for the kinetic characterisation of TPI
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Experimental data set for the kinetic characterisation of the glucose transport reaction
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Experimental data set for the kinetic characterisation of PK
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Experimental data for the phosphoglycerate mutase (EC 5.4.2.12) activity.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creator: Theresa Kouril
Submitter: Theresa Kouril
Timecourses of GLC (starting at 5 mM) and LAC, PYR, GLY in the closed system.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creator: Abeer Fadda
Submitter: Abeer Fadda
Creator: Abeer Fadda
Submitter: Abeer Fadda
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
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 ...
Creator: Abeer Fadda
Submitter: Abeer Fadda
WT 110901_SN865_B_L006_R1_GQC-28- ATCACG.fastq.gz 100 19.624.852 1,29
llumina fastq format 4 lines for each sequence: 1- Unique identifier, with the following format: @::::#/ 2- Sequence (A, T, C ,G or N (undetermined) only) 3- Orientation (always forward without mapping) 4- Quality value for each base, corresponding to a Phred-like score encoded in ASCII format, with an offset of of 33 (e.g. “J” gives a value of 41) and is in accordance with sanger FASTQ format. The sequence file is compressed ...
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
See wild type sample.
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
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.
Creator: Alejandro Leroux
Submitter: Alejandro Leroux
This data file shows results from the different chemostat experiments.Gene expression rates are presented.
Creators: Katja Bettenbrock, Sonja Steinsiek
Submitter: Katja Bettenbrock
Mutants with defects in glucose transport systems were analyzed in a bioreactor and the transcription of certain uptake systems analyzed. Transcription profiles between batch and chemostat conditions were compared
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
Creator: Katja Bettenbrock
Submitter: Katja Bettenbrock
by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels
Creator: Katja Bettenbrock
Submitter: Katja Bettenbrock
The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.
Creator: Katja Bettenbrock
Submitter: Katja Bettenbrock
Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR
Creator: Katja Bettenbrock
Submitter: Katja Bettenbrock
RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the ...
Creators: None
Submitter: Leif Steil
Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.
Creators: None
Submitter: Olga Krebs
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.
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
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/).
Creator: Anna Feldman-Salit
Submitter: Anna Feldman-Salit
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: The JERM Harvester
batch fermatation - The transition from growing to non-growing Bacillus subtilis cells
Creator: Sandra Maass
Submitter: Sandra Maass
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.
Creators: Sandra Maass, Michael Kohlstedt, Claudia Korneli
Submitter: Sandra Maass
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.
Creator: Sandra Maass
Submitter: Sandra Maass
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.
Creator: Sandra Maass
Submitter: Sandra Maass
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.
Creators: Sandra Maass, Michael Kohlstedt, Claudia Korneli
Submitter: Sandra Maass