FlopR: An open source software package for calibration and normalization of plate reader and flow cytometry data

• DOI: 10.5281/zenodo.3977408
• Publication Date: 2020-08-27
• Authors: Alex J. H. Fedorec; Clare Robinson; Ke Yan Wen; C. Barnes
• Keywords: Normalization

AbstractThe measurement of gene expression using fluorescence markers has been a cornerstone of synthetic biology for the last two decades. However, the use of arbitrary units has limited the usefulness of this data for many quantitative purposes. Calibration of fluorescence measurements from flow cytometry and plate reader spectrophotometry has been implemented previously but the tools are disjointed. Here we pull together, and in some cases improve, extant methods into a single software tool, written as a package in the R statistical framework. The workflow is validated usingEscherichia coliengineered to express GFP from a set of commonly used constitutive promoters. We then demonstrate its power by identifying the time evolution of distinct subpopulations of bacteria from bulk plate reader data, a task previously reliant on laborious flow cytometry experiments. Along with standardized parts and experimental methods, the development and dissemination of usable tools for quantitative measurement and data analysis will benefit the synthetic biology community by improving interoperability.Graphical Abstract