OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
- Jonathan L. Schmid-Burgk1,3,
- Tobias Schmidt1,3,
- Moritz M. Gaidt1,
- Karin Pelka2,
- Eicke Latz2,
- Thomas S. Ebert1 and
- Veit Hornung1
- 1Institute of Molecular Medicine, University Hospital, University of Bonn, 53127 Bonn, Germany;
- 2Institute of Innate Immunity, University Hospital, University of Bonn, 53127 Bonn, Germany
- Corresponding author: veit.hornung{at}uni-bonn.de
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↵3 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.176701.114.
- Received April 2, 2014.
- Accepted July 14, 2014.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.