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Nat Methods. 2018 Apr;15(4):271-274. doi: 10.1038/nmeth.4604. Epub 2018 Feb 19.

On the design of CRISPR-based single-cell molecular screens.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
2
Howard Hughes Medical Institute, Seattle, Washington, USA.

Abstract

Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.

PMID:
29457792
PMCID:
PMC5882576
DOI:
10.1038/nmeth.4604
[Indexed for MEDLINE]
Free PMC Article

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