Large-scale Image-based Profiling of Single-cell Phenotypes in Arrayed CRISPR-Cas9 Gene Perturbation Screens

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2018 Jan 25

PMID 29363560

Citations 33

Authors

Reinoud de Groot

Joel Luthi

Helen Lindsay

Rene Holtackers

Lucas Pelkmans

Affiliations

Soon will be listed here.

Abstract

High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9.

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