CRISPR/Cas9 Screening to Identify Conditionally Essential Genes in Human Cell Lines.

Autor:	Huggler KS; Morgridge Institute for Research, Madison, WI, USA.; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA., Rossiter NJ; Morgridge Institute for Research, Madison, WI, USA., Flickinger KM; Morgridge Institute for Research, Madison, WI, USA.; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA., Cantor JR; Morgridge Institute for Research, Madison, WI, USA. jcantor@morgridge.org.; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. jcantor@morgridge.org.; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA. jcantor@morgridge.org.; University of Wisconsin Carbone Cancer Center, Madison, WI, USA. jcantor@morgridge.org.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2377, pp. 29-42.
DOI:	10.1007/978-1-0716-1720-5_2
Abstrakt:	Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells. However, most such screens have been performed in vitro with little consideration into how medium composition might affect gene essentiality. This protocol describes a method to use CRISPR/Cas9-based loss-of-function screens to ask how gene essentiality in human cell lines varies with medium composition. First, a single-guide RNA (sgRNA) library is packaged into lentivirus, and an optimal infection titer is determined for the target cells. Following selection, genomic DNA (gDNA) is extracted from an aliquot of the transduced cells. The remaining transduced cells are then screened in at least two distinct cell culture media. At the conclusion of the screening period, gDNA is collected from each cell population. Next, high-throughput sequencing is used to determine sgRNA barcode abundances from the initial and each of the final populations. Finally, an analytical pipeline is used to identify medium-essential candidate genes from these screen results. (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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