PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media
PHENOS: a high-throughput and flexible tool for microorganism growth phenotyping on solid media
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PHENOS：一种高通量、灵活的固体培养基微生物生长表型分析工具
DOI：
10.1101/195784
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Barton D
中科院分区：
文献类型：
--
作者：
Barton D
微生物阵列以机器人的精度在单个平板上打印大量不同的菌株，为越来越多的遗传和基因组方法提供了基础。这些技术包括合成遗传阵列分析、高通量定量性状位点（QTL）分析和双杂交技术。测量这些阵列中单个菌落的生长是许多这些技术的重要组成部分，但对任何阵列工作都很有用。测量通常使用输入复杂图像分析软件的间歇性图像来完成，这不是特别准确，并且很难有效地使用。我们已经开发了一种简单而快速的替代技术，使用一个钉钉机器人和一个普通的微孔板阅读器来连续测量固体琼脂上生长的菌落的厚度，辅以一种技术来规范最初打印到阵列每个点上的细胞数量。我们已经开发了软件来自动组合多组读数，减去琼脂吸光度，并以多种信息方式可视化菌落厚度变化的过程。结果针对酵母菌优化的“PHENOS”管道（PHENotyping On Solid media）可产生高度可重复性的生长曲线，并且对低水平生长特别敏感。我们已经根据经验确定了一个公式来估计集落细胞计数从吸光度测量，并表明这是可比的估计从液体测量。我们还通过复制传统液体表型的早期QTL研究结果验证了该技术，并发现PHENOS相当敏感。结论“PHENOS”是一种成本有效、可靠的高通量技术，用于酵母阵列的定量生长，可能同样非常适用于一系列其他类型的微生物阵列。有关管道和软件的详细指南随安装文件附在https://github.com/gact/phenos上。
BackgroundMicrobial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and genomic approaches. These include Synthetic Genetic Array analysis, high-throughput Quantitative Trait Loci (QTL) analysis and 2-hybrid techniques. Measuring the growth of individual colonies within these arrays is an essential part of many of these techniques but is useful for any work with arrays. Measurement is typically done using intermittent imagery fed into complex image analysis software, which is not especially accurate and is challenging to use effectively. We have developed a simple and fast alternative technique that uses a pinning robot and a commonplace microplate reader to continuously measure the thickness of colonies growing on solid agar, complemented by a technique for normalizing the amount of cells initially printed to each spot of the array in the first place. We have developed software to automate the process of combining multiple sets of readings, subtracting agar absorbance, and visualizing colony thickness changes in a number of informative ways.ResultsThe “PHENOS” pipeline (PHENotyping On Solid media), optimized forSaccharomycesyeasts, produces highly reproducible growth curves and is particularly sensitive to low-level growth. We have empirically determined a formula to estimate colony cell count from an absorbance measurement, and shown this to be comparable with estimates from measurements in liquid. We have also validated the technique by reproducing the results of an earlier QTL study done with conventional liquid phenotyping, and found PHENOS to be considerably more sensitive.Conclusions“PHENOS” is a cost effective and reliable high-throughput technique for quantifying growth of yeast arrays, and is likely to be equally very useful for a range of other types of microbial arrays. A detailed guide to the pipeline and software is provided with the installation files at https://github.com/gact/phenos .
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DOI：
--
发表时间：
2013
期刊：
影响因子：
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作者：
Kume;T.;Tanaka;N.;Kuraji;K.;Komatsu;H.;Yoshifuji;N.;Saitoh;T. M.;Suzuki;M. and Kumagai;T.;Kazuhiro Sato
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影响因子：
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