Assays
264 Assays visible to you, out of a total of 528This 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.
Contributor: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Dear SEEK users, this Assay is just an example Excel sheet for intracellular metabolites concentration measurements performed using cell culture growing in chemostat
Contributor: Olga Krebs
Assay type: Metabolite Profiling
Technology type: Mass Spectrometry
Snapshots: No snapshots
These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.
Contributor: Daniel Seaton
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.
Contributor: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Snapshots: No snapshots
Contributor: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Snapshots: No snapshots
Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.
Contributor: Daniel Seaton
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Contributor: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Snapshots: No snapshots
Plant material
The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for
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Contributor: Daniel Seaton
Assay type: Protein Quantification
Technology type: Mass Spectrometry
Snapshots: No snapshots
Transcript profiling by microarray in 4, 6, 8, 12 and 18 h photoperiods, originally published in Flis et al, 2016, Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. doi: 10.1111/pce.12754.
Contributor: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Snapshots: No snapshots
BPG degradation at 70C
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Collection for experimental SOPs
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Measurements of external metabolites based on growth curve data.
Flux estimates for uptake of external metabolites such as glucose and production rates for external metabolites lactate and acetate
Contributor: Niels Zondervan
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
Snapshots: No snapshots
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Proteomics data for L.ferriphilum samples (continuous and with mineral)
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
RNAseq data for L.ferriphilum samples
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Here we will use JERM templates with embedded ontologies to describe and annotate example data
Contributor: Olga Krebs
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Jan-Willem Veening
Assay type: Experimental Assay Type
Technology type: Next generation sequencing
Snapshots: No snapshots
Contributor: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Snapshots: No snapshots
Contributor: Dawie Van Niekerk
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Mutants with a linear respiratory chain consisting of NADH Dehydrogenase II and one of the terminal oxidases cytochrom bo, cytochrome bd I or cytochrome bd II were growth in chemostats with defined oxygen supply. The amounts of biomass formed and of acetate and formate produced were determined.
Contributor: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Chemostat Measurement
Snapshots: No snapshots
Mutants with linear respiratory chains were grown under SUMO chemostat conditions at different defined aerobiosis levels. The ArcA phoshorylation state as determined.
Contributor: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Gel Electrophoresis
Snapshots: No snapshots
Experimental data for the conversion of 3PG to F6P and the gluconeogenic pathway intermediates
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase
Contributor: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase
Contributor: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots