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Dissecting Molecular Phenotypes Through FACS-Based Pooled CRISPR Screens

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Embryonic Stem Cell Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2520))

Abstract

Pooled CRISPR screens are emerging as a powerful tool to dissect regulatory networks, by assessing how a protein responds to genetic perturbations in a highly multiplexed manner. A large number of genes are perturbed in a cell population through genomic integration of one single-guide RNA (sgRNA) per cell. A subset of cells with the phenotype of interest can then be enriched through fluorescence-activated cell sorting (FACS). SgRNAs with altered abundance after phenotypic enrichment allow identification of genes that either promote or attenuate the investigated phenotype. Here we provide detailed guidelines on how to design and execute a pooled CRISPR screen to investigate molecular phenotypes. We describe how to generate a custom sgRNA library and how to perform a FACS-based screen using readouts such as intracellular antibody staining or Flow-FISH to assess phosphorylation levels or RNA abundance. Through the variety of available perturbation systems and readout options many different molecular and cellular phenotypes can now be tackled with pooled CRISPR screens.

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Author information

Author notes

  1. Oriana Genolet and Liat Ravid Lustig contributed equally with all other contributors.

Authors and Affiliations

  1. Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany

    Oriana Genolet, Liat Ravid Lustig & Edda G. Schulz

Authors
  1. Oriana Genolet
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  2. Liat Ravid Lustig
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  3. Edda G. Schulz
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Corresponding author

Correspondence to Edda G. Schulz .

Editor information

Editors and Affiliations

  1. Ottawa, ON, Canada

    Kursad Turksen

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Genolet, O., Ravid Lustig, L., Schulz, E.G. (2022). Dissecting Molecular Phenotypes Through FACS-Based Pooled CRISPR Screens. In: Turksen, K. (eds) Embryonic Stem Cell Protocols . Methods in Molecular Biology, vol 2520. Humana, New York, NY. https://doi.org/10.1007/7651_2021_457

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  • DOI: https://doi.org/10.1007/7651_2021_457

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2436-4

  • Online ISBN: 978-1-0716-2437-1

  • eBook Packages: Springer Protocols

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