PT  - JOURNAL ARTICLE
AU  - Paul Datlinger
AU  - Christian Schmidl
AU  - André F Rendeiro
AU  - Peter Traxler
AU  - Johanna Klughammer
AU  - Linda Schuster
AU  - Christoph Bock
TI  - Pooled CRISPR screening with single-cell transcriptome read-out
AID  - 10.1101/083774
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 083774
4099  - http://biorxiv.org/content/early/2016/10/27/083774.short
4100  - http://biorxiv.org/content/early/2016/10/27/083774.full
AB  - CRISPR-based genetic screens have revolutionized the search for new gene functions and biological mechanisms. However, widely used pooled screens are limited to simple read-outs of cell proliferation or the production of a selectable marker protein. Arrayed screens allow for more complex molecular read-outs such as transcriptome profiling, but they provide much lower throughput. Here we demonstrate CRISPR genome editing together with single-cell RNA sequencing as a new screening paradigm that combines key advantages of pooled and arrayed screens. This approach allowed us to link guide-RNA expression to the associated transcriptome responses in thousands of single cells using a straightforward and broadly applicable screening workflow.