Studies

Short Name: 04_stPanTr Title: Solanum tuberosum Pan-Transcriptome Description: Solanum tuberosum Pan-Transcriptome Raw Data: pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak Principal investigator: Kristina Gruden License: CC BY 4.0 Sharing permission: Public Upload to FAIRDOMHub: Yes

Supplementary Information linked together

A repository of causal cellular signalling statement

A guidelines for the curation of molecular interactions causal statements.

One pot cascade - pathway analysis for the purified Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, removal of XLA, and optimisation on Xylose to aKG is studied.

https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate

This study contains our single nuclei characterisation of whole hearts from Fzt.DU mice published in Cells.

Supplemental files for the publication of the dataset collection.

Initial rate kinetics for the purified Caulinobacter crescentus Weimberg pathway enzymes, including substrate dependence, and product inhibition.

Progress curves for the purified Caulinobacter crescentus Weimberg pathway enzymes. Each reaction is followed up to completion and then the next enzyme in the pathway is added, i.e. XDH-XLA-XAD-KDXD and finally KGSADH

Cell free extract - pathway analysis for Caulinobacter crescentus Weimberg pathway enzymes. Effect of co-factor recycling, and Mn2+ on Xylose to aKG conversion is studied.

The model is an extensio of PLM_67v3 with an additional an additional variable Temp in ODE 25. This change allows to simulated warm pulses that affect EC stability using COPASI. 

Originally submitted to PLaSMo on 2014-03-10 13:16:25

Model that eliminates several light inputs. RVE8, NOX are incorporated. Individual representation of CCA1 and LHY. Several changes in conections and light inputs. Fogelmark reports eight parameter sets. This SBML file contains the first parameter set Related PublicationsFogelmark K, Troein C (2014). Rethinking transcriptional activation in the Arabidopsis circadian clock.. PLoS Comput Biology. Retrieved from: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003705Originally ...

To map genome wide transcriptome responses in Atlantic cod PCLS treated with BaP and EE2. See Yadetie et al., 2018.

Study: _S_03_stCuSTr Short Name: 03_stCuSTr Title: Solanum tuberosum Cultivar-Specific Transcriptomes Description: Solanum tuberosum Cultivar-Specific Transcriptomes Raw Data: ../_S_01_sequences/, ../_S_02_denovo/ pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED FILES: /reports/README.MD https://fairdomhub.org/documents/346 /_STUDY_METADATA.TXT ...

Study: _S_02_denovo Short Name: 02_denovo Title: De novo assemblies Description: De novo assemblies for cration of potato reference transcriptomes Raw Data: ../_S_01_sequences/ pISA Study creation date: 2019-10-23 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED FILES: /reports/README.MD https://fairdomhub.org/documents/343 /_STUDY_METADATA.TXT https://fairdomhub.org/documents/342 ...

Study: _S_01_sequences Short Name: 01_sequences Title: NGS sequences for de novo assembly Description: NGS sequences for de novo assembly; input for Study 02_denovo Raw Data: see: ./reports/SupplementaryTableS1-Input_sequences_information.xlsx pISA Study creation date: 2019-10-23 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes

RELATED FILES: /reports/README.MD ...

Predictions made using the core model for combinatorial perturbations to the model simulating combined effects from OE, KO mutants, perturbations and time series concentrations.

Internal metabolites concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations External metabolite concentrations for time series data (not pulse experiments) and for mutant OE, KO mutants and perturbations Mutant (OE, KO, perturbation) metabolite measurements

Training of the core model, parameter estimation using Evolutionary Programming using metabolomics, proteomics and some flux data. The core model contains reactions in glycolysis, pyruvate metabolism and ATPase

Validation of the core model of glycolysis, pyruvate metabolism and ATPase reaction using OE, KO mutant samples and perturbation samples

This section contains all the raw data and files required for each figures.

Determination of thermophysical properties (densities, diffusion coefficients, energy contributions) of different methanol-water mixtures using molecular dynamics simulations.

Assays for model composition here, in order to share model files; potentially training and validation data in other Studies.