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OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines.

ABSTRACT: The application of designer nucleases allows the induction of DNA double-strand breaks (DSBs) at user-defined genomic loci. Due to imperfect DNA repair mechanisms, DSBs can lead to alterations in the genomic architecture, such as the disruption of the reading frame of a critical exon. This can be exploited to generate somatic knockout cell lines. While high genome editing activities can be achieved in various cellular systems, obtaining cell clones that contain all-allelic frameshift mutations at the target locus of interest remains a laborious task. To this end, we have developed an easy-to-follow deep sequencing workflow and the evaluation tool OutKnocker (www.OutKnocker.org), which allows convenient, reliable, and cost-effective identification of knockout cell lines.

SUBMITTER: Schmid-Burgk JL

PROVIDER: S-EPMC4199374 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines.

Schmid-Burgk Jonathan L JL Schmidt Tobias T Gaidt Moritz M MM Pelka Karin K Latz Eicke E Ebert Thomas S TS Hornung Veit V

Genome research 20140903 10

The application of designer nucleases allows the induction of DNA double-strand breaks (DSBs) at user-defined genomic loci. Due to imperfect DNA repair mechanisms, DSBs can lead to alterations in the genomic architecture, such as the disruption of the reading frame of a critical exon. This can be exploited to generate somatic knockout cell lines. While high genome editing activities can be achieved in various cellular systems, obtaining cell clones that contain all-allelic frameshift mutations a ...[more]

PMID: 25186908

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