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Cluse LA, Nikolic I, Knight D, Madhamshettiwar PB, Luu J, Cowley KJ, Semple T, Arnau GM, Shortt J, Johnstone RW, Simpson KJ. A Comprehensive Protocol Resource for Performing Pooled shRNA and CRISPR Screens. Methods Mol Biol 2018; 1725:201-227. [PMID: 29322420 DOI: 10.1007/978-1-4939-7568-6_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This chapter details a compendium of protocols that collectively enable the reader to perform a pooled shRNA and/or CRISPR screen-with methods to identify and validate positive controls and subsequent hits; establish a viral titer in the cell line of choice; create and screen libraries, sequence strategies, and bioinformatics resources to analyze outcomes. Collectively, this provides an overarching resource from the start to finish of a screening project, making this technology possible in all laboratories.
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Affiliation(s)
- Leonie A Cluse
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Deborah Knight
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Piyush B Madhamshettiwar
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jennii Luu
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Karla J Cowley
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Timothy Semple
- Molecular Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Gisela Mir Arnau
- Molecular Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Jake Shortt
- School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia.
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