Open AccessFlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data
Author(s) -
Alex J H Fedorec,
Clare Robinson,
Ke Wen,
C. Barnes
Publication year - 2020
Publication title -
acs synthetic biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.156
H-Index - 66
ISSN - 2161-5063
DOI - 10.1021/acssynbio.0c00296
Subject(s) - workflow , software , computer science , normalization (sociology) , synthetic biology , r package , extant taxon , data mining , calibration , flow cytometry , computational biology , biology , biological system , mathematics , statistics , database , genetics , programming language , evolutionary biology , sociology , anthropology
The measurement of gene expression using fluorescence markers has been a cornerstone of synthetic biology for the past two decades. However, the use of arbitrary units has limited the usefulness of these 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 using Escherichia coli engineered to express green fluorescent protein (GFP) from a set of commonly used constitutive promoters. We then demonstrate the package's power by identifying the time evolution of distinct subpopulations of bacteria from bulk plate reader data, a task previously reliant on laborious flow cytometry or colony counting 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.