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3421 Data files visible to you, out of a total of 5622

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the the M-loop region of a Leishmania donovani alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering). No result was obtained for compound 6.

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the interface region between two neighboring alpha-tubulin monomers of Leishmania donovani; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Leishmania donovani alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...

Leishmania donovani multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of L. donovani alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the M-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Leishmania infantum; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region ...

Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).

The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger ...

Leishmania infantum multimeric alpha-tubulin protein receptor for docking studies, generated by alignment of two identical models of L. infantum alpha-tubulin on template 5ubq alpha-tubulin chains of two neighboring protofilaments (A, C).

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

Submitter: Anette McLeod

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

Creator: Anette McLeod

Submitter: 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

Submitter: 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

Submitter: Anette McLeod

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

Creator: Anette McLeod

Submitter: Anette McLeod

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

Creator: Anette McLeod

Submitter: Anette McLeod

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

Creator: Anette McLeod

Submitter: Anette McLeod

Experimental data, in MATLAB binary file format.

Biomass and metabolite data for Laurel and Hardy 1.

Model simulation data for Laurel and Hardy 1, in MATLAB binary format.

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on ...

Complete excel spradsheets for Laurel and Hardy 2, including data for the pgm mutant that were not analysed in the Chew et al. 2017 preprint/publication. Data include fresh and dry biomass, gas exchange, leaf numbers and metabolites in Col0 (WT), prr7prr9, pgm and lsf1 plants. Metabolite data are from plants after 27 days of growth (end of night) and 28 days (end of day and end of night).

Experimental data for Laurel and Hardy 2, in MATLAB binary format.

Mean and SD data for metabolites and biomass, along with metadata used to simulate this experiment.

Simulation data for Laurel and Hardy 2, in MATLAB binary format.

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on ...

Excel spreadsheets for biomass, leaf number, gas exchange and metabolites, including pgm and lhycca1. Key data are for 27-28 day old plants for Col and prr7prr9, analysed for the preprint/publication. Gas exchange data for lhycca1 showed lower Assimilation per unit area than Col, prr7prr9; A in pgm was higher than Col. Metabolite data were also collected for Col and lhycca1 at 18 days, before the lhycca1 flowered, but these are marked as unreliable.

Experimental data for Laurel and Hardy 3, in MATLAB binary format.

Simulation data for Laurel and Hardy 3, in MATLAB binary format.

Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.

Starch levels in carbon units (not C6) measured on on days ...

Experimental data set for the kinetic characterisation of LDH

Data for Fig. Supp 7B in Chew et al. PNAS 2014 Leaf number of the growing rosettes, from 5 to 37 days after sowing. Data and also results of three FMv1 model simulations, with default, fitted and linear (i.e. no juvenile-adult transition in phyllochron)

Data for Figs 3C, 3F and Supp 2 in Chew et al. PNAS 2014 Leaf number of the growing rosettes, from 4 to 37 days after sowing (DAS). Data and also results of FMv1 model simulations. Note that Fei-0 was previously tested by Mendez-Vigo et al, suggesting this line had a higher leaf appearance rate. We suggested that its larger final leaf number was more likely due to faster germination.

This excel template is for use of describing HCS microscopy data. It was created based on ISA methodology and modified to conform REMBI recomandations.

Comparison between axenic and planktonic readcounts with deseq2

Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta

Comparison for LFQs with t-test in Perseus

Repository for omics data analysis

Table combining data for L.ferriphilum. RNAseq data, Proteomics LFQs, Functional annotation

No description specified
No description specified
No description specified
No description specified

LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed

LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed

Raw read files for samples

Normalized counts (tpm) for L.ferriphilum samples from continuous culture.

Normalized counts (tpm) for LF samples with mineral

Raw data and assembly for pacbio sequencing of L.ferriphilum.

LFQ intensities derived from proteomics measurements

No description specified

Linked with model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Linked with model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Linked with Model: 10.15490/fairdomhub.1.model.802.1

Creators: None

Submitter: James Wordsworth

Data file for PLaSMo accesssion ID PLM_4, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Submitter: BioData SynthSys

Salmon feed switch experiment: Lipid class quantitation for gut tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipid class quantitation for liver tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipid class quantitation for muscle tissue samples (POS mode).

Lipid class abbreviations used: CE, cholesterol esters FC, free cholesterol Cer, ceramides HexCer, hexosyl ceramides (ie. galactosyl and glucosyl ceramides) MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols SM, sphingomyelins.

Salmon feed switch experiment: Lipid identification for gut tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' prefix ...

Salmon feed switch experiment: Lipid identification for liver tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

Salmon feed switch experiment: Lipid identification for muscle tissue samples (POS mode).

Lipid abbreviations used: CE, cholesterol esters Cer, ceramides GalCer, galactosyl ceramides GluCer, glucosyl ceramides MG, monoacylglycerols DG, diacylglycerols TG, triacylglycerols LPE, lysophosphatidylethanolamines LPC, lysophosphatidylcholines PC, phosphatidylcholines PE, phosphatidylethanolamines PG, phosphatidylglycerols PI, phosphatidylinositols PS, phosphatidylserines SM, sphingomyelins.

The 'O-' ...

No description specified

Results of lipid species (expressed in pmol) determined in cod liver microsomes exposed to PAH and PFAS

Full list of detected miRNA which were found to be deregulated in PE-EVs.

Creator: Natalia Gebara

Submitter: Natalia Gebara

Participants of 2nd FAIRDOM PALs meeting in Munich

List of participants/1st EraSysApp PALs meeting

Creator: Olga Krebs

Submitter: Olga Krebs

List of publications from 2006 till 2016. Note: I retired from the University of Amsterdam in 2010

Creator: Roel Van Driel

Submitter: Roel Van Driel

This Excel file contains lists of model (Comprehensive model for COVID-19) reactions and species in table format Comprehensive model for COVID-19 coused by SARS-CoV-2

Publications and patents from the last 6 years

No description specified

Creator: Stefan Henrich

Submitter: Stefan Henrich

Concentrations of various contaminants in liver from cod caged in Kollevåg and at reference location.

Creators: None

Submitter: Karina Dale

EROD activity in liver of cod exposed to chlorpyrifos-methyl

Creator: Karina Dale

Submitter: Karina Dale

Mean normalized expression (MNE) levels of cyp1a and acox1 measured in liver of Atlantic Cod exposed to PAH and PFAS mixtures

Creator: Karina Dale

Submitter: Karina Dale

FPKMs or Fragments Per Kilobase of exon per Million reads . Fragment means fragment of DNA, so the two reads that comprise a paired-end read count as one. Per kilobase of exon means the counts of fragments are then normalized by dividing by the total length of all exons in the gene (or transcript). This bit of magic makes it possible to compare Gene A to Gene B even if they are of different lengths. Per million reads means this value is then normalized against the library size. This bit of magic ...

PDB file of the prepared Leishmania major dihydrofolate reductase docking receptor based on a published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without water molecules.

PDB file of the prepared Leishmania major pteridine reductase 1 docking receptor based on chain A of PDB-ID 1e92 with a conserved set of structural waters.

PDB file of the prepared Leishmania major pteridine reductase 1docking receptor based on chain A of PDB-ID 1e92 without additional water molecules.

Batch sample publishing

Creators: None

Submitter: Jake Schissel

Data for local pH monitoring experiments for dissolution in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution

Data for local pH monitoring precipitation experiments in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution

Local sensitivity analysis based on 40 samples using 1000x sampling from measurement distribution. The control shown is the control over flux through glycolysis represented by flux through PRK. Th plot summarized the control for each parameter over all observed metabolite concentrations encountered for the 40 samples. As such the metabolic control analysis is local but shows the distribution taking into account measurement error as well as biological variation over the 40 samples.

Tab seperated file containing the raw output of the local sensitivity analysis based on 40 samples (based on 1000x sampled metabolite values) from the MEAN and SD of the metabolite measurements. Sensitivity analysis is based on the flux through PFK as objective and as proxy for flux through glycolysis. Data can be plotted using the R script "plotLocalGlobalSensitivity1.5.R" associated to the same assay.

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

Creator: Paul Heusden

Submitter: Paul Heusden

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

Creator: Paul Heusden

Submitter: 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

Submitter: Paul Heusden

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

Creator: Paul Heusden

Submitter: 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

Submitter: Paul Heusden

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

Creator: Paul Heusden

Submitter: Paul Heusden

First selection of LOINC Codes for data extraction

No description specified

Raw data for L.ferriphilum biofilm proteomics data

Raw proteomics data for L. ferriphilum planktonic samples

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