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.
Preview |
Text
Bahler_High-Throughput, High-Precision Colony Phenotyping with Pyphe_AAM.pdf - Accepted Version Download (239kB) | Preview |
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 |
Archive Staff Only
 |
View Item |
