Assays
What is an Assay?Filters
intracellular metabolite measured by GC/MS and LC/MS
Submitter: Hanna Meyer
Assay type: Metabolomics
Technology type: NMR
Investigation: Multiomics study of Bacillus subtilis under osm...
Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Creating data sheet template for 'omics data
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Investigation: Creating data sheet template for 'omics data
Some examples of transcriptomics templates for NimbleGen data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to GEO/ArrayExpress upon publication and greater consistency of data in SEEK for easier searching and comparing.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Electrophoresis
Investigation: Creating data sheet template for 'omics data
This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression. 3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the ...
Submitter: Abeer Fadda
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Gene expression in Trypanosoma brucei
- Preparation of B. subtilis cultures
Inoculate cells from -80°C stocks in 10 ml time-lapse microscopy (TLM) medium (62 mM K2HPO4 , 44mM KH2PO4, 15 mM (NH4)2SO4, 6.5 mM sodium citrate, 0.8 mM MgSO4, 0.02 % casamino acids, 27.8 mM glucose, 0.1 mM L-tryptophan, the pH was set to 7 using a KOH solution) supplemented with antibiotics, if necessary. Grow the cells overnight in a shake flask (30°C, 225 rpm). The following morning, dilute the cells 1:10 in pre-warmed chemically defined medium (CDM) (62 ...
Submitter: Jan-Willem Veening
Assay type: Experimental Assay Type
Technology type: Imaging
Investigation: Wetlab approach to transcription fidelity
S. pyogenes wildetype, an arcA- and a glnA-deletion mutants were grown in CDM-LAB cultures at pH 6.5 and 7.5 and at a growth rate of 0.05
Submitter: Antje Sieg
Assay type: Experimental Assay Type
Technology type: HPLC
Investigation: Amino acid metabolism of four LAB species: Stre...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Investigation on the effect of pulsed metabolit...
In order to construct an in vivo-like buffer for S. pyogenes, the intracellular concentrations of Fe, K, Mg, Mn Na, P and S elements were determined via ICP-AES (inductively coupled plasma atomic emissionspectroscopy) method at the Institute of Land Use, University of Rostock. The samples for the analysis were obtained from a steady state culture grown on CDM-LAB with glucose.
Submitter: Araz Zeyniyev
Assay type: Metabolite Profiling
Technology type: Inductively Coupled Plasma Mass Spectrometry
Investigation: Amino acid metabolism of four LAB species: Stre...
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods. Cell leakage and metabolite recovery was determined by ATP measurements
Submitter: John Raedts
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
Submitter: John Raedts
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
Submitter: Daniel Hönicke
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Altering the expression pattern in Clostridium ...
Submitter: Federico Rojas
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Perturbing the biological system: developmental...
This assay is designed to obtain the in vitro kinetic data of T. brucei recombinant trypanothione synthetase. The enzyme catalyzes the ATP-dependent ligation of spermidine (Spd) and GSH to generate glutathionylspermidine (Gsp) and also of Gsp and GSH to finally produce trypanothione (T(SH)2). The data was obtained in an spectrophotometric assay that links ADP production with NADH consumption through the piruvte kinase and lactate dehydrogenase.
Submitter: Alejandro Leroux
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Investigation: Kinetic understanding of the T. brucei trypanot...
Submitter: Federico Rojas
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Perturbing the biological system: developmental...
This assay is for method development to quantify intra- and extra-cellular metabolites on T. brucei 427 bloodstream form using isotope ratio based MS technique with 13C-labelled E. coli extract
Submitter: Dong-Hyun Kim
Assay type: Metabolite Concentration
Technology type: Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Study: Metabolic flux measurement
Intracellular metabolites in T. brucei at different stage of cell growth have been quantified absolutely by isotope ratio based MS technique using uniformly 13C-labelled E. coli extract. This is the case study for method development of absolute quantification for metabolic flux analysis.
Submitter: Dong-Hyun Kim
Assay type: Metabolomics
Technology type: Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Study: Metabolic flux measurement
Metabolite profiling on T. brucei exposed to methylene blue has been carried out using LC-MS to investigate metabolic changes caused by oxidative stress
Submitter: Dong-Hyun Kim
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
26 intracellular metabolites (amino acids, polyamines, TCA intermediates) in T. brucei exposed to methylene blue have been absolutely quantified using isotope ratio based MS technique.
Submitter: Dong-Hyun Kim
Assay type: Intracellular Metabolite Concentration
Technology type: Isotope Ratio Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
26 intracellular metabolites (amino acids, polyamines, TCA intermediates) in T. brucei under pH stress (pH8.7) have been absolutely quantified using isotope ratio based MS technique.
Submitter: Dong-Hyun Kim
Assay type: Intracellular Metabolite Concentration
Technology type: Isotope Ratio Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Study: Targeted metabolite analysis
Extracellular metabolites in T. brucei at different stage of cell growth have been quantified absolutely by isotope ratio based MS technique using uniformly 13C-labelled E. coli extract. This is the case study for method development of absolute quantification for metabolic flux analysis.
Submitter: Dong-Hyun Kim
Assay type: Extracellular Metabolite Concentration
Technology type: Isotope Ratio Mass Spectrometry
Investigation: Metabolite profiling, quantification and flux q...
Study: Metabolic flux measurement
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Identification of targets of the essential RNas...
Glucose transporter mutants were analyzed under aerobic and aerobic conditions in batch cultures with glucose as substrate. Acetate formation rates and glucose consumption rates were measured, as well as extracellular cAMP concentrations.
Submitter: Sonja Steinsiek
Assay type: Extracellular Metabolite Concentration
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
Mutant strains which lack one or more of the glucose transport systems were analyzed in aerobic chemostat cultures and compared to batch cultures.
Submitter: Sonja Steinsiek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
MG1655 and mutant strains with defects in glucose transport systems were analyzed in aerobic and anaerobic batch cultures.
Submitter: Sonja Steinsiek
Assay type: Gene Expression Profiling
Technology type: Technology Type
Investigation: Analysis of the glucose transport in Escherichi...
Submitter: Michael Ederer
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...