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

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%.

SUBMITTER: Hill AJ

PROVIDER: S-EPMC5882576 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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

Hill Andrew J AJ McFaline-Figueroa José L JL Starita Lea M LM Gasperini Molly J MJ Matreyek Kenneth A KA Packer Jonathan J Jackson Dana D Shendure Jay J Trapnell Cole C

Nature methods 20180219 4

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%. ...[more]

PMID: 29457792

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On the design of CRISPR-based single cell molecular screens

Project description:We demonstrate that vector designs for such screens that rely on cis linkage of guides and distally located barcodes suffer from swapping of intended guide-barcode associations at rates approaching 50% due to template switching during lentivirus production, greatly reducing sensitivity.

2018-01-29 | GSE108699 | GEO

On the design of CRISPR-based single cell molecular screens

Project description:On the design of CRISPR-based single cell molecular screens

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Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens.

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GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens.

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Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer.

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