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High-Throughput, High-Precision Colony Phenotyping with Pyphe

Kamrad, S; Bähler, J; Ralser, M; (2022) High-Throughput, High-Precision Colony Phenotyping with Pyphe. Yeast Functional Genomics , 2477 pp. 381-397. 10.1007/978-1-0716-2257-5_21. Green open access

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Abstract

Colony fitness screens are powerful approaches for functional genomics and genetics. This protocol describes experimental and computational procedures for assaying the fitness of thousands of microbial strains in numerous conditions in parallel. Data analysis is based on pyphe, an all-in-one bioinformatics toolbox for scanning, image analysis, data normalization, and interpretation. We describe a standard protocol where endpoint colony areas are used as fitness proxy and two variations on this, one using colony growth curves and one using colony viability staining with phloxine B. Different strategies for experimental design, normalization and quality control are discussed. Using these approaches, it is possible to collect hundreds of thousands of data points, with low technical noise levels around 5%, in an experiment typically lasting 2 weeks or less.

Type: Article
Title: High-Throughput, High-Precision Colony Phenotyping with Pyphe
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1007/978-1-0716-2257-5_21
Publisher version: https://doi.org/10.1007/978-1-0716-2257-5_21
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher's terms and conditions.
Keywords: Screen, Colony, Fitness, Functional genomics, Phenomics, Microbiology, Python software, large-scale phenotyping, Cell viability, Growth curve
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10164410
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