Included in crispr, rnaseq, singlecell_rna_sequencing themes

Pooled CRISPR screening with single-cell transcriptome read-out


Created on 29th October 2016

Paul Datlinger; Christian Schmidl; Andre F Rendeiro; Peter Traxler; Johanna Klughammer; Linda Schuster; Christoph Bock;


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.

Show more

Review Summary

# Status Date