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Depositordc.contributorMarkakis, Konstantinos
Funderdc.contributor.otherGlaxoSmithKlineen_UK
Funderdc.contributor.otherIndustrial Biotechnology Innovation Centre
Funderdc.contributor.otherEPSRC - Engineering and Physical Sciences Research Council
Spatial Coveragedc.coverage.spatialEdinburghen_UK
Spatial Coveragedc.coverage.spatialUKen
Spatial Coveragedc.coverage.spatialUNITED KINGDOMen
Time Perioddc.coverage.temporalstart=2016-10-01; end=2017-02-02; scheme=W3C-DTFen
Data Creatordc.creatorMarkakis, Konstantinos
Data Creatordc.creatorDe Las Heras, Aitor
Date Accessioneddc.date.accessioned2017-06-12T13:48:22Z
Date Availabledc.date.available2017-06-12T13:48:22Z
Citationdc.identifier.citationMarkakis, Konstantinos; De Las Heras, Aitor. (2017). OD and Fluorescent measurements for the experiments included in "An analytical approach for the calculation of promoter activities based on fluorescent protein expression data", 2016-2017 [dataset]. University of Edinburgh, School of Engineering, Institute of Bioengineering. https://doi.org/10.7488/ds/2063.en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/2732
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2063
Dataset Description (abstract)dc.description.abstractThe systematic prediction and categorisation of promoters, repressors, enhancers, etc., is not only essential to unravel the inner workings of biochemical networks, but also to engineer novel synthetic ones. Each putative regulatory region, however, has to be validated experimentally in order to be categorized as a fully defined functional element, which constitutes a significant bottleneck. In most studies, the promoter activity is illustrated as the amount of fluorescence divided by the optical density. These values are obtained from a coupled time-series experiment. With relatively simple mathematical reasoning, a tool that describes promoter activity in each time point has been implemented. The protein expression and the protein maturation process are modelled as a first order differential equations taking into account the degradation and the maturation rates which are to be known in advance. The promoter activity is then expressed based on the measured quantities of optical density and fluorescence with a formula derived by mathematical manipulations of the defined quantities and the differential equations that comprise the model. The continuous expressions for fluorescence and optical density are obtained from Gaussian process regression. Validation with experimental data from several constructs showed the expected behaviour of promoter activities. The dataset consists of 3 files, 2 of them are CSV files and ready to be imported in the software tool presented in the publication and one of them is an excel file of raw data from a plate reader containing OD and fluorescent measurements.en_UK
Dataset Description (TOC)dc.description.tableofcontents- Data_for_figure_3.csv : Contains measurements of OD and Fluorescence for the constitutive promoters presented in figure 3. - Data_for_figure_4.csv: Contains measurements of OD and Fluorescence for the inducible promoters presented in figure 4. - Data_for_figure_5.csv: Contains measurements of OD and Fluorescence for the constitutive promoter and stable/unstable GFP presented in figure 5.en_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh, School of Engineering, Institute of Bioengineeringen_UK
Rightsdc.rightsCreative Commons Attribution 4.0 International Public Licenseen
Subjectdc.subjectGaussian processen_UK
Subjectdc.subjectBacterial growth modellingen_UK
Subjectdc.subjectpromoter activityen_UK
Subjectdc.subjectScreening strategiesen_UK
Subjectdc.subjectStandardisationen_UK
Subjectdc.subjectOptimisationen_UK
Subjectdc.subjectGenetic Circuitsen_UK
Subjectdc.subjectIn silico modelsen_UK
Subjectdc.subjectMeasurementen_UK
Subjectdc.subjectFluorescent proteinsen_UK
Subjectdc.subjectregression modelen_UK
Subject Classificationdc.subject.classificationEngineering::Bioengineeringen_UK
Titledc.titleOD and Fluorescent measurements for the experiments included in "An analytical approach for the calculation of promoter activities based on fluorescent protein expression data"en_UK
Typedc.typedataseten_UK

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