OD and Fluorescent measurements for the experiments included in "An analytical approach for the calculation of promoter activities based on fluorescent protein expression data"

  • Konstantinos Markakis (Creator)
  • Aitor De Las Heras (Creator)

Dataset

Abstract

The 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.

Data Citation

Markakis, 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. http://dx.doi.org/10.7488/ds/2063.
Date made available12 Jun 2017
PublisherEdinburgh DataShare
Temporal coverage1 Oct 2016 - 2 Feb 2017

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