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ScMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens.

ABSTRACT: We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel functions in cell proliferation, and enables an unbiased construction of genotype-phenotype network. Single-cell CRISPR screening on mouse embryonic stem cells identifies key genes associated with different pluripotency states. Applying scMAGeCK on multiple datasets, we identify key factors that improve the power of single-cell CRISPR screening. Collectively, scMAGeCK is a novel tool to study genotype-phenotype relationships at a single-cell level.

SUBMITTER: Yang L

PROVIDER: S-EPMC6979386 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens.

Yang Lin L Zhu Yuqing Y Yu Hua H Cheng Xiaolong X Chen Sitong S Chu Yulan Y Huang He H Zhang Jin J Li Wei W

Genome biology 20200124 1

We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel functions in cell proliferation, and enables an unbiased construction of genotype-phenotype network. Single-cell CRISPR screening on mouse embryonic stem cells identifies key genes associated with diffe ...[more]

PMID: 31980032

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