CRISPR screening with single-cell RNA-seq readout


CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.


Pooled CRISPR screening with single-cell transcriptome readout

Pooled CRISPR screening with single-cell transcriptome readout

Datlinger P, Schmidl C, Rendeiro A, Krausgruber T, Traxler P, Klughammer J, Schuster L, Kuchler A, Alpar D, Bock C

Nature Methods  14, 297-301 (2017). DOI: 10.1038/nmeth.4177

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* shared first or shared senior authorship