New paper in Nature Methods establishing CRISPR screens with single-cell transcriptome readout

We provide proof-of-concept for single-cell CRISPR screening as a new approach that combines key strengths of pooled and arrayed screens, and we validated CROP-seq as a flexible and straightforward method for performing such screens. We expect CROP-seq to be broadly useful for studying biological mechanisms that are difficult to reduce to a simple readout needed for classical pooled screens.

Paul Datlinger, André F Rendeiro*, Christian Schmidl*, Thomas Krausgruber, Peter Traxler, Johanna Klughammer, Linda C Schuster, Amelie Kuchler, Donat Alpar, Christoph Bock# (2016). Pooled CRISPR screening with single-cell transcriptome readout. Nature Methods. DOI: 10.1038/nmeth.4177

*shared first author   # corresponding author

Abstract: 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. (no journal subscription? Read it online for free or ask us to send you the PDF)