Assays

263 Assays visible to you, out of a total of 516

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.

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

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.

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
...

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.

BPG degradation at 70C

Contributor: Jacky Snoep

Assay type: Metabolite Concentration

Technology type: Technology Type

Snapshots: No snapshots

Collection for experimental SOPs

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

No description specified

Contributor: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

RNAseq data for L.ferriphilum samples

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

No description specified

Contributor: Theresa Kouril

Assay type: Experimental Assay Type

Technology type: Enzymatic Activity Measurements

Snapshots: No snapshots

No description specified
No description specified

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.

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

Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase

Mutant strains with linear electron transport chain were grown in chemostat cultures at different defined aerobiosis levels. Expression of selected genes was determined by Real Time RT-PCR

No description specified
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