Data files
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Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Creators: Alexey Kolodkin, Hans V. Westerhoff, Raju Prasad Sharma
Submitter: Alexey Kolodkin
Volumes in fL, time in hours.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
The abscissa of the plots shows the percentage of aerobiosis that is a physiological measure for oxygen availability (http://www.ncbi.nlm.nih.gov/pubmed/11844770).
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Grey Boxes: Enzymes & Reactions blue lines/symbols: flux in mmol per gramm dry cell weight an hour red lines/symbols: mRNA levels
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White Boxes: Intracellular and extracellular metabolites blue lines/symbols: concentration of the metabolites (extracellular: mM, intracellular: AU)
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Yellow Boxes: Aggregated Quantities as yield, ...
Creator: Michael Ederer
Submitter: Michael Ederer
This file contains the IDs, adj. p-values and official gene names of the top 100 marker genes (where applicable) for each of the identified cluster.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Master file, aggregates metabolite concentrations inside and outside the cell, protein copy number and flux estimates for metabolites in the core model. Based on all internal metabolite concentrations, external metabolite concentrations from growth curve data, flux of glucose, lactate and acetate based on growth curve data and protein copy number data for enzyme concentrations. Combines absolute and relative measurements and metabolomics measurements from different experiment to get an as complete ...
Creator: Niels Zondervan
Submitter: Niels Zondervan
Master template for hands on session
Creator: Olga Krebs
Submitter: Olga Krebs
Data file for PLaSMo accesssion ID PLM_1010, version 1
Creators: BioData SynthSys, Daniel Seaton
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_70, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 1
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 3
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_64, version 4
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_76, version 1
Creators: BioData SynthSys, Yin Hoon Chew, Yin Hoon
Submitter: BioData SynthSys
Data file for PLaSMo accesssion ID PLM_6, version 2
Creators: BioData SynthSys, Alexandra Pokhilko, Andrew Millar
Submitter: BioData SynthSys
. L. lactis (NZ9000), E. faecalis (V538) and S. pyogenes (M49) wild type strain and their ldh- mutants were grown in batch cultures at 37°C in anaerobic 96 wells plates in either TH-broth supplemented with 0.5% (w/v) yeast (THY) or a chemically defined medium for LAB (pH 7.4) (CDM-LAB (10)). Both media were buffered with either 100 mM MES buffer or 100 mM MOPS buffer for growth at pH 6.5 and 7.5 respectively.
Creators: Martijn Bekker, Tomas Fiedler
Submitter: Martijn Bekker
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Linked with model: DOI: 10.15490/fairdomhub.1.model.801.1
Creators: None
Submitter: James Wordsworth
Linked to model: DOI: 10.15490/fairdomhub.1.model.800.1
Creators: None
Submitter: James Wordsworth
Linked to model: DOI: 10.15490/fairdomhub.1.model.799.1
Creators: None
Submitter: James Wordsworth
Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(R) except CO2, which is in parts of the partial pressure.
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Steady state concentrations of intracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(CV).
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Steady state metabolic fluxes measured in glucose-limited chemostat of Saccharomyces cerevisiae at D = 0.1 h-1 growing on minimal medium. Fluxes are: glucose, ethanol, glycerol, acetate, succinate, pyruvate, lactate, citrate, malate, a-ketoglutarate, fumarate
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
Heterologous Expression of LDHs from different lactic acid bacteria in Escherichia coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model .
Creators: None
Submitter: Silvio Hering
Heterologous Expression of LDH from L.actis (MG1363) in E. coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model
Creator: Wayne Aubrey
Submitter: Wayne Aubrey
Crosslinl (URL) to Gitlab info site on COVID-19 (University Medical Center Göttingen, Department of Medical Informatics)
Creators: Harald Kusch, Theresa Bender, Christian Bauer
Submitter: Harald Kusch
Meeting location map
Creator: Olga Krebs
Submitter: Olga Krebs
none
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
TRK1, TRK2
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
AFG3, AKR1, BRP1, COG6, ERG6, HRK1, LST7, NHX1, PEP5, PIG1, PTK2, RCK2, RCY1, REF2, RIC1, RTS1, SGF11, SAP185, SKY1, SNC2, SUR2,
Creator: Silvia Petrezselyova
Submitter: The JERM Harvester
The membrane fraction of Prorcentrum cordatum was prepared and proteins solubilized using SDS. Subsequently, proteins were separated by SDS-PAGE, subjected to tryptic in-gel digest and nanoLC ESI-iontrap MS/MS.
Creators: None
Submitter: Lars Wöhlbrand
First MESI-STRAT Newsletter June 2019
Creators: Petra Engele, Kathrin Thedieck, Tobias Anzeneder, Janina Leyk
Submitter: Petra Engele
Untargeted and targeted metabolic analysis on T. b. brucei 427 grown under oxidative stress with methylene blue has been carried out. This work has been completed with 11 bio-reps and found significant metabolic changes as you can see in the IDEOM file attached. 'Comparison' tab in the data spread sheet shows heat maps and fold change analysis regarding different metabolite levels (T: T brucei, TMB: T. brucei exposed to methylene blue, numbers: time points, 0, 5, 60 & 120min). If you double ...
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Creator: Margrete Solheim
Submitter: Margrete Solheim
Creator: Margrete Solheim
Submitter: Margrete Solheim
Contains: -Relative metabolite measurements at different time points from all experiments -Absolute metabolite measurements for amino-acid analysis of the proteome and the cytosol -Effect on adding CaCl2, KCl or NaCl to the medium on growth -Effect of spiking of growth medium with additional amino acids
Creators: Niels Zondervan, Luis Serrano, Maria Lluch, Eva Yus
Submitter: Niels Zondervan
Creator: Jacqueline Wolf
Submitter: Jacqueline Wolf
SysMo2: Intra- and extracellular metabolome data of the chemostat experiments: nitrogen limitation, nitrogen limitation+ NaCl, nitrogen limitation + glucose
Creator: Hanna Meyer
Submitter: Hanna Meyer
Intracellular metabolome analysis of S. solfataricus P2 grown on caseinhydrolysate or D-glucose as sole carbon source. Samples were analyzed with GC-MS. CoA derivatives were analyzed with LC-MS.
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Creators: Katy Wolstencroft, Olga Krebs
Submitter: Katy Wolstencroft
A file which combine previous metabolomics samples ID to new sample ID file (https://fairdomhub.org/data_files/1330)
Overview of metabolomics results from liver of cod exposed to chlorpyrifos-methyl
Creator: Karina Dale
Submitter: Karina Dale
Column 1: Row numbers Column 2: Sample id (See below) Column 3: Water (Fish from salt water or fresh water) Column 4: Tissue (Liver or Gut) Column 5: Feed (MA- Marine oil, VO- Vegetable oil) Column 6: Day Column 7: Count file location
Column 2 explained: The freshwater fish have no tank numbers and saltwater fish do have tank numbers eg : 69-D0-MA-G-1 - > 69 well position (id given when sequncing), Day 0, Marine oil, Gut, Fish number 1 147-D16-VO-MA-L-6 -> 147 well position, Day 16, Vegetable ...
Creators: Graceline Tina Kirubakaran, Gareth Gillard
Submitter: Graceline Tina Kirubakaran
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P1_SxPv10vsSxP12/_A_RootsSxPv10vsv12-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
Metall Stress
Creator: Susanne Gerber
Submitter: The JERM Harvester
Very simple unrealistic values for Metformin kinetics (Km). For use in a simple graphical model.
Creator: Hannah O'Keefe
Submitter: Hannah O'Keefe
The file describe the methodology of the used algorithm to calculate the sensitivities against knockout and over-expression perturbations. The sensitivity values were classified in macro values for every perturbation. The bitwise distances were calculated for each biomolecule in the same macro class
Creator: Ahmed Hemedan
Submitter: Ahmed Hemedan
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Creator: Jan-Willem Veening
Submitter: Jan-Willem Veening
Master table describing all the samples included in MOA Investigation; studies are descrubed using MIAPPE (Minimum Information About a Plant Phenotyping Experiment).
Creators: None
Submitter: Ziva Ramsak
File describing the phenotypic observations taken on potato plants, namely spot necroses, vein necroses, chlorotic spots, yellowing and mechanicam damage.
Creators: None
Submitter: Ziva Ramsak
Archive containing some phenotyping images (.tar.gz).
Creator: Ziva Ramsak
Submitter: Ziva Ramsak
Measurements of photosynthetic activity, namely net photosynthesis (Pn), stomatal conductance (Cond), actual photochemical efficiency (Fv’/Fm’), potential photochemical activity (Fv/Fm), chlorophyll content (SPAD) and electron transport rate (ETR).
Creators: None
Submitter: Ziva Ramsak
Statistical analysis of measurements of photosynthetic parameters.
Creators: None
Submitter: Ziva Ramsak
qPCR measured values of Potato virus Y (PVY).
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA Investigation sample ID's and GEO sample identifiers.
Creators: None
Submitter: Ziva Ramsak
Differential expression of genes between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Creators: None
Submitter: Ziva Ramsak
QC filtered and RSN normalised values for all MOA samples with microarray measurements.
Creators: None
Submitter: Ziva Ramsak
Code used for the analysis of microarray data.
Creator: Ziva Ramsak
Submitter: Ziva Ramsak
Some additional files required for the R code (phenodata, feature data i.e. the GAL file and Agi4x44PreProcess downloaded package, as it is not maintained on BioConductor anymore).
Creator: Ziva Ramsak
Submitter: Ziva Ramsak
Validation of microarray results by RT-qPCR. RT-qPCR measurements for eight genes: biologically relevant for photosynthesis chlorophyll a-b binding protein (CAB, CAB_NEW) and RuBisCO activase (RA); for defense response three classes of β-1,3-glucanases (Glu-I, Glu-II, Glu-III) and pathogenesis-related protein1b (PR-1b); and for sugar metabolism granule bound starch synthase I (GBSSI) and cell wall invertase (INV).
Creators: None
Submitter: Ziva Ramsak
RT-qPCR assays for microarray validation described using the MIQE standard.
Creators: None
Submitter: Ziva Ramsak
miRNA stem-loop RT-qPCR for sRNA-Seq data validation. sRNA expression results obtained by sRNA-seq were validated by stem-loop RT-qPCR. For validation experiments, the same RNA samples as used for sRNA-Seq were analysed.
Creators: None
Submitter: Ziva Ramsak
RT-qPCR assays for sRNA-Seq validation described using the MIQE standard.
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA sample identifiers to GEO identifiers related to sRNAomics dataset.
Creators: None
Submitter: Ziva Ramsak
miRNAs and their counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
miRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
Differential expression of miRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Creators: None
Submitter: Ziva Ramsak
phasiRNAs and their counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
phasiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
Differential expression of phasiRNAs between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given.
Creators: None
Submitter: Ziva Ramsak
R code for differential expression analysis of sRNA-Seq.
Creator: Ziva Ramsak
Submitter: Ziva Ramsak
vsiRNAs and their counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
vsiRNAs and their RPM normalised counts identified in the MOA samples for sRNA-Seq.
Creators: None
Submitter: Ziva Ramsak
Novel miRNAs and/or novel MIR loci identified in PVYNTN- and mock-inoculated samples of cv. Désirée and NahG-Désirée potato plants. List of novel/known miRNAs with novel MIR loci. For each miRNA, sequence, length, class (C – conserved or N – novel), miRNA family, the genome locations, strand, the predicted hairpin precursor (pre-miRNA) sequences and the location in genome (MIR loci), their lengths, minimal folding energy index (MFEI; calculated as described by Zhang et al. (2006) as well as gene ...
Creators: None
Submitter: Ziva Ramsak
PHAS loci identified by genome and transcriptome-wide phasing analysis. List of genome locations for the all identified non-coding PHAS loci or transcript identifiers (IDs) for protein-coding PHAS loci together with the lengths of their producing phasiRNAs. For the protein-coding PHAS loci, transcript full description, protein domains (obtained from PFAM database; Finn et al. 2016), MapMan ontology annotation (from GoMapMan;(Ramšak et al. 2014)) and log2 ratio of gene expression between PVYNTN-infected ...
Creators: None
Submitter: Ziva Ramsak
sRNA regulatory network connecting endogenous miRNAs, phasiRNAs and their targets.
Creators: None
Submitter: Ziva Ramsak
sRNA regulatory network connecting miRNAs, phasiRNAs, PVY-derived siRNAs (vsiRNAs) and their targets.
Creators: None
Submitter: Ziva Ramsak
Predicted targets of endogenous small RNAs (sRNAs) by in silico approach. For each predicted interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, short gene name, full descriptions, MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) and predicted target regulation (cleavage or translational repression) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier ...
Creators: None
Submitter: Ziva Ramsak
Table connecting MOA degradome pool identifiers to GEO identifiers.
Creators: None
Submitter: Ziva Ramsak
Experimentally validated targets of endogenous sRNAs by Degradome-Seq. For each identified interaction, miRNAs/phasiRNA ID, the target transcript identifiers, representative gene identifier, full descriptions, and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each sRNA-target interaction, degradome category ...
Creators: None
Submitter: Ziva Ramsak
Targets of PVY-derived siRNAs identified by Degradome-Seq. For each predicted interaction, PVYNTN-derived siRNAs (vsiRNAs), the target transcript identifiers, representative gene identifier, full descriptions and MapMan ontology annotations (GoMapMan; (Ramšak et al., 2014)) are shown. Short names for potato genes were inferred from Arabidopsis thaliana orthologs where applicable, else the StNIB_v1 gene identifier was set (Ramšak et al., 2014). For each vsiRNA-target interaction, degradome category ...
Creators: None
Submitter: Ziva Ramsak
List of identified proteins and their counts; using MaxQuant software for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for MaxQuant quantified proteins.
Creators: None
Submitter: Ziva Ramsak
List of identified peptides using MaxQuant software for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
List of identified proteins and their counts; using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
Differentially expressed proteins between various comparison groups (Sheet: comparisons), with log2-fold changes and Benjamini-Hochberg FDR corrected p-values given for spectral count (Proteome Discoverer) quantified proteins.
Creators: None
Submitter: Ziva Ramsak
List of identified peptides using spectral counts (Proteome Discoverer) for selected MOA proteomics pool identifiers.
Creators: None
Submitter: Ziva Ramsak
Concentrations of seven different plant hormones (ABA, GA3, OPDA, JA, IAA and SA) as determined by gas chromatography coupled with mass spectrometry (GC-MS) for MOA samples.
Creators: None
Submitter: Ziva Ramsak
Significant changes for a set of hormones between treatment-genotype groups as determined by ANOVA followed by LSD post hoc analysis (FDR < 0.05) using the Agricolae R package.
Creators: None
Submitter: Ziva Ramsak
R code for the hormone analysis.
Creator: Ziva Ramsak
Submitter: Ziva Ramsak
The metano scenario file for aerobic growth on 3-Hydroxybenzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on 3-Hydroxybenzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on 4HPP.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on 4HPP.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on acetate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on acetate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on Benzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on benzoate.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for aerobic growth on L-phenylalanine.
Creators: None
Submitter: Julia Koblitz
The metano scenario file for anaerobic growth on L-phenylalanine.
Creators: None
Submitter: Julia Koblitz
Creators: Meina Neumann-Schaal, Dietmar Schomburg, Julia Koblitz
Submitter: Julia Koblitz
Comparative flux balance analysis file. All values are given in mmol/g/h. Fluxes were optimized to maximize BIOMASS.
Creators: None
Submitter: Julia Koblitz
Uptake and growth rates, and biomass yields are compared in vivo and in silico.
Creators: None
Submitter: Julia Koblitz
Contains all 10 parameter sets, loaded with proteomics measurements for three time points (6h,24h, 48h). Contains all parameter sets exported from COPASI, an overview of the parameter sets in the three conditions and how well they perform as well as scripts to load parameter sets as well as an R script to generate an overview of the model error in predicting for all 10 parameter sets.
Creator: Niels Zondervan
Submitter: Niels Zondervan
The figure contains information necessary to understand the mathematical model of experiments in BSA115. In these experiments sigB response is artificially initiated by the addition of IPTG while sigB is downstream of a Pspac promoter. The figure shows a flow-chart diagram that combines three hypotheses to explain experiments. It contains the ODEs and the fit of the respective models to the data.
Creator: Ulf Liebal
Submitter: Ulf Liebal
The modelling workflow used on the input data, which leads to the results, see associated publication.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
- MNT-021_Bl6J_J-20-0152_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-022_Bl6J_J-20-0154_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-023_Bl6J_J-20-0156_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-024_Bl6J_J-20-0158_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-025_Bl6J_J-20-0160_CYP2D6- 1/3000_Run ...
Creators: Uta Dahmen, Mohamed Albadry
Submitter: Mohamed Albadry
- MNT-021_Bl6J_J-20-0152_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-022_Bl6J_J-20-0154_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-023_Bl6J_J-20-0156_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-024_Bl6J_J-20-0158_CYP2D6- 1/3000_Run 14_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_004 > Control
- MNT-025_Bl6J_J-20-0160_CYP2D6- 1/3000_Run ...
Creators: Uta Dahmen, Mohamed Albadry
Submitter: Mohamed Albadry
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
mRNAs with decreased abundance in all replicates with an average fold change of at least 1.5
Creators: None
Submitter: Leif Steil
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_0
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_10
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_40
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_5
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_60
Creator: Dani Valverde
Submitter: The JERM Harvester
MS001_90
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_0
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_10
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_40
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_5
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_60
Creator: Dani Valverde
Submitter: The JERM Harvester
MS002_90
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_0
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_10
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_40
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_5
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_60
Creator: Dani Valverde
Submitter: The JERM Harvester
MS003_90
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ andlong timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_0
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_10
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_40
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_5
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_60
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS004_90
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_0
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_10
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_10
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_40
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_5
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_60
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS005_90
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_0
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_20
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_40
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_5
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_60
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS006_90
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and long timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS007_1
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS007_12
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS007_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS007_6
Creator: Dani Valverde
Submitter: The JERM Harvester
MS007_8
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS008_05
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS008_12
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS008_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS008_6
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS008_8
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_0
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_12
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_12
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_6
Creator: Dani Valverde
Submitter: The JERM Harvester
MS009_8
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 50mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS010_1
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS010_12
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS010_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS010_6
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS010_8
Creator: Dani Valverde
Submitter: The JERM Harvester
MS011_1
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS011_12
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS011_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS011_6
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS011_8
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS012_1
Creator: Dani Valverde
Submitter: The JERM Harvester
MS012_12
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS012_4
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
MS012_6
Creator: Dani Valverde
Submitter: The JERM Harvester
MS012_8
Creator: Dani Valverde
Submitter: The JERM Harvester
Growth yeast with 0mM K+ and short timing collection
Creator: Dani Valverde
Submitter: The JERM Harvester
Clustal Omega multiple sequence alignment result for selected alpha-tubulins in FASTA format with gaps. Species and corresponding Uniprot identifiers can be found in the FASTA file.
The following species (Uniprot ID, dinitroaniline-sensitive/resistant) were considered:
- Trypanosoma cruzi (Q27352, sensitive)
- Trypanosoma brucei brucei (Q4GYY5, sensitive)
- Leishmania infantum (E9AGJ8, sensitive)
- Leishmania donovani (I3W8N6, sensitive)
- Leishmania major (Q4QGC5, sensitive)
- Toxoplasma gondii ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Clustal Omega multiple sequence alignment result for selected beta-tubulins in FASTA format with gaps. Species and corresponding Uniprot identifiers can be found in the FASTA file.
The following species (Uniprot ID, dinitroaniline-sensitive/resistant) were considered:
- Trypanosoma cruzi (Q8STF3, sensitive)
- Trypanosoma brucei brucei (Q4GYY6, sensitive)
- Leishmania infantum (A4HZJ3, sensitive)
- Leishmania donovani (I3W8N7, sensitive)
- Leishmania major (Q4QBZ6, sensitive)
- Toxoplasma gondii ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Batch sample publishing
Creators: None
Submitter: Dikshant Pradhan
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Fatty acid methyl ester (FAME) analysis showing which fatty acids were in the samples, though not what specific lipids they were part of (triacylglycerides, phospholipids, etc.) https://en.wikipedia.org/wiki/Fatty_acid_methyl_ester
Values in Ark1!A2:AO21 are probably mass percent of total FAME, including C19:0 added for calibration. Sample identifiers are lab-local; GSF1 identifiers are in Ark5!A4:U22 but suffer from typos. Use caution and see below.
This workbook is a mess:
- Results appear in ...
Creators: Magny Sidsel Thomassen, Sandve Simen, Jacob Seilø Torgersen, Jon Olav Vik, Arne Gjuvsland
Submitter: Magny Sidsel Thomassen
Creator: Jake Schissel
Submitter: Jake Schissel