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The calculation of amino acid uptake rates for cells of Sulfolobus solfataricus P2 grown on caseinhydrolysate was performed based on the relative consumption of individual amino acids from the growth medium and the previously published absolute concentration of amino acids in the used growth medium.

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

Submitter: Martijn Bekker

  • Calculations of predictions of all identified proteins of P. cordatum
  • Calculations of fold-changes of all identified proteins (cell vs. nuclei fraction) of P. cordatum
  • Calculations of predictions of proteins of unknown function of_ P. cordatum_
  • Calculations of fold-changes of unknowns (cell vs. nuclei fraction) of P. cordatum

Tab color: all identified proteins, purple; unkowns, green

Creators: None

Submitter: Jana Kalvelage

14CO2 assimilation in the night-time, in plants of Col, prr7prr9; Ws, lhycca1 genotypes at 18 and 28 days, and partitioning among cellular fractions.

It is a description of the maternal clinical data, fetal Doppler ultrasound data and delivery data of both groups of cases (late-onset fetal growth restriction) and controls (normal growth).

Creator: Gabriela Loscalzo

Submitter: Gabriela Loscalzo

It is a description of the maternal clinical data, fetal Doppler ultrasound data and delivery data of both groups of cases (late-onset fetal growth restriction) and controls (normal growth).

Creator: Gabriela Loscalzo

Submitter: Gabriela Loscalzo

No description specified

Creator: Joerg Stuelke

Submitter: 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

Submitter: Leif Steil

The file contains an UMAP representation illustrating the expression of the stem cell marker Cd34 in all identified cell clusters.

Batch sample publishing

Cell volume_trk_

Creator: Silvia Petrezselyova

Submitter: 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.

Batch sample publishing

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, and additional Mn2+ (0.15 mM) added.

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, without NAD recycling, but with additional Mn2+ (0.15 mM) added.

Data files for the conversion of XYL to KG, in Caulobacter crescentus cell free extract, with NAD recycling, but without additional Mn2+ added.

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

Submitter: Martijn Bekker

No description specified
No description specified

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.

Batch sample publishing

Contains CML dictionaries created to store deep eutectic solvent data with CML.

Contains CML created for experimental, simulation and predicted data. Predictions were made based on experimental data using a gradient boosting decision tree.

No description specified

Combined taxonomy table of abundance of OTUs (Operational Taxonomy Units) in both freshwater and saltwater samples from 16S V3-V4 Illumina sequencing of gut microbiota. Primers used for sequencing are given in https://fairdomhub.org/sops/270 The OTUs are presented in number of counts per sample (n=349). Each row represent one sample. Raw data are available in the Sequence Read Archive database under accession number SRP119730 (https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP119730).

RNAseq data file, source: /mnt/users/fabig/DigiSal/crispr_RNAseq/samples_ELOVL2/final/2018-06-25_samples_ELOVL2/combined.counts

Tail intensities (%) measured by the Comet Assay as indication of DNA fragmentation in blood cells of Atlantic cod exposed to PAHs and PFASs

Creator: Karina Dale

Submitter: Karina Dale

Photos of drop test conpresed in .zip file

Creator: Jaromir Zahrádka

Submitter: The JERM Harvester

nha1, ena1-5, double deletion

Creator: Jaromir Zahrádka

Submitter: 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/).

Comparison of Kcat values model and values from literature. Model values are based on Vmax enzyme parameters (maximum activity per enzyme molecule). Literature values are largely based on whole cell enzyme extract assays and do not take into account allosteric control. In addition activity is measured at varying time points and varying conditions. The error based on differences in enzyme concentrations at different time points and the error in protein copy number measurements is taken into account ...

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

Comparison of model SS metabolite concentrations with measured values using 1000x sampling from the Gausian distribution of the measured values based on multiple replicates per measured conditions. Graphs showing the distribution of measured and simulated metabolite concentration for 95 mutand (KO, OE), perturbation and time series measurements. Model simulations performed using 24h proteomics with modification of enzyme parameters for KO and OE mutants.

Analysis of the sequences of PGM1 from several Synechocystis strains revealed a different annotation for Synechocystis sp. PCC 6803, which included a 16-amino acid N-terminal extension that is missing in the other strains. Additionally, the experimentally validated transcriptional start site from Synechocystis sp. PCC 6803 suggests a shorter open reading frame for PGM1, with Met 17 as putative translational start site. To clarify if the N-terminal extension is an annotation error, we prepared ...

Creator: Sofia Doello

Submitter: Sofia Doello

Culture conditions along with substrate and product compositions throughout the culture.

No description specified
No description specified

Creators: None

Submitter: Marta Eide

No description specified

Creators: None

Submitter: Marta Eide

No description specified

Creators: None

Submitter: Marta Eide

No description specified

Creators: None

Submitter: Marta Eide

No description specified

Creators: None

Submitter: Marta Eide

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

Table with InterPro annotations, matches to Pcitri.v1 genome and differential expression between mated and virgin P.citri females for the transcripts in the consolidated P. citri transcriptome.

Creator: Mojca Juteršek

Submitter: Mojca Juteršek

Transcriptome sequences merged from de novo assembly and IsoSeq sequence data.

Creator: Mojca Juteršek

Submitter: Mojca Juteršek

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.

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

Submitter: 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 ...

Data file for PLaSMo accesssion ID PLM_64, version 3

Data file for PLaSMo accesssion ID PLM_70, version 2

Data file for PLaSMo accesssion ID PLM_7, version 2

Data file for PLaSMo accesssion ID PLM_83, version 1

Data file for PLaSMo accesssion ID PLM_84, version 1

Data file for PLaSMo accesssion ID PLM_85, version 1

Data file for PLaSMo accesssion ID PLM_86, version 1

Data file for PLaSMo accesssion ID PLM_87, version 1

Data file for PLaSMo accesssion ID PLM_88, version 1

Data file for PLaSMo accesssion ID PLM_89, version 1

Data file for PLaSMo accesssion ID PLM_89, version 2

Data file for PLaSMo accesssion ID PLM_90, version 1

Data file for PLaSMo accesssion ID PLM_91, version 1

Data file for PLaSMo accesssion ID PLM_92, version 1

Data file for PLaSMo accesssion ID PLM_77, version 1

Data file for PLaSMo accesssion ID PLM_78, version 1

Data file for PLaSMo accesssion ID PLM_79, version 1

Data file for PLaSMo accesssion ID PLM_70, version 1

No description specified

In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 45,000 scholarly articles, including over 33,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.

This dataset is intended to mobilize researchers to apply recent advances in natural language processing to generate new insights in ...

Creator: Allen Institute For AI, Anthony Goldbloom, Peijen Lin, Paul Mooney, Carissa Schoenick, Sebastian Kohlmeier, devrishi, Timo Bozsolik, Ben Hamner

Submitter: Martin Golebiewski

DOI: 10.15490/fairdomhub.1.datafile.3719.1

Quantification of CPM and TCP concentrations in cod liver and bile using gas chromatography

Creator: Karina Dale

Submitter: Karina Dale

Meta data file, Source: /mnt/users/fabig/DigiSal/crispr_RNAseq/meta/crispr_metadata.txt

The structure of was Transaminase of gamma-proteobacterium deposited in PDB under the code: 7p3t

Creator: Eleni Konia

Submitter: Ioannis Metaxas

Contains exp.csv, a collection of experimental data of CholineChloride:Glycerol:Water mixtures. Contains sim.csv, a collection of molecular dynamics simulation data of CholineChloride:Glycerol:Water mixtures. Contains Modelling_exp_Figure3.csv, a collection of modelled Eeta (energy activation of viscous flow), lnEta0 (viscosity at infinite temperature) values of CholineChloride:Glycerol:Water mixtures, based on experimental data, see the associated publication for details. Contains ...

The classification in reproducible and not reproducible models was made by Tiwari et al.

Citations were looked up in Scopus, Web of Science and Google Scholar.

The following journals had to be excluded, as Journal Impact Factors (JIF) were missing or papers were discontinued:

  • Experientia was closed 1996 and continued as Cellular and Molecular Life Sciences 1997
  • The American journal of physiology – split into fields 1977, further splits in 1980 and 1989
  • IFAC Proceedings Volumes – last issue ...

Creator: Matthias König

Submitter: Matthias König

Creator: Matthias König

Submitter: Matthias König

Measured in cod liver by the ELISA method, in Atlantic cod exposed to PAHs and PFASs

Creator: Karina Dale

Submitter: Karina Dale

CYP1A2: Generic Classification 128

CYP2E1: Generic Classification 128

CYP3A4: Generic Classification 128

TRK1, TRK2

Creator: Silvia Petrezselyova

Submitter: The JERM Harvester

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