FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.,ACS Synthetic Biology

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FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry Data.
ACS Synthetic Biology ( IF 3.7 ) Pub Date : 2020-08-27 , DOI: 10.1021/acssynbio.0c00296
Alex J H Fedorec ₁ , Clare M Robinson ₁ , Ke Yan Wen ₁ , Chris P Barnes _{1,

2}

Affiliation

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.

中文翻译：

FlopR：用于校准和标准化读板器和流式细胞术数据的开源软件包。

在过去的二十年里，使用荧光标记测量基因表达一直是合成生物学的基石。然而，任意单位的使用限制了这些数据对于许多定量目的的有用性。流式细胞术和酶标仪分光光度法的荧光测量校准以前已经实施过，但这些工具是脱节的。在这里，我们将现有方法整合到一个软件工具中，并在某些情况下进行改进，以 R 统计框架中的包形式编写。使用经改造的大肠杆菌从一组常用的组成型启动子表达绿色荧光蛋白 (GFP)，对工作流程进行了验证。然后，我们通过从散装板读取器数据中识别不同细菌亚群的时间演化来展示该软件包的功能，这项任务以前依赖于费力的流式细胞术或菌落计数实验。除了标准化部件和实验方法之外，用于定量测量和数据分析的可用工具的开发和传播将通过提高互操作性使合成生物学界受益。

更新日期：2020-09-20

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