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

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 ex...

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Autores principales: Schmid-Burgk, Jonathan L., Schmidt, Tobias, Gaidt, Moritz M., Pelka, Karin, Latz, Eicke, Ebert, Thomas S., Hornung, Veit
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Resource
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199374/
https://www.ncbi.nlm.nih.gov/pubmed/25186908
http://dx.doi.org/10.1101/gr.176701.114
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author Schmid-Burgk, Jonathan L.
Schmidt, Tobias
Gaidt, Moritz M.
Pelka, Karin
Latz, Eicke
Ebert, Thomas S.
Hornung, Veit
author_facet Schmid-Burgk, Jonathan L.
Schmidt, Tobias
Gaidt, Moritz M.
Pelka, Karin
Latz, Eicke
Ebert, Thomas S.
Hornung, Veit
author_sort Schmid-Burgk, Jonathan L.
collection PubMed
description 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.
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spelling pubmed-41993742015-04-01 OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines Schmid-Burgk, Jonathan L. Schmidt, Tobias Gaidt, Moritz M. Pelka, Karin Latz, Eicke Ebert, Thomas S. Hornung, Veit Genome Res Resource 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. Cold Spring Harbor Laboratory Press 2014-10 /pmc/articles/PMC4199374/ /pubmed/25186908 http://dx.doi.org/10.1101/gr.176701.114 Text en © 2014 Schmid-Burgk et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ 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/.
spellingShingle Resource
Schmid-Burgk, Jonathan L.
Schmidt, Tobias
Gaidt, Moritz M.
Pelka, Karin
Latz, Eicke
Ebert, Thomas S.
Hornung, Veit
OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title_full OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title_fullStr OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title_full_unstemmed OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title_short OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
title_sort outknocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199374/
https://www.ncbi.nlm.nih.gov/pubmed/25186908
http://dx.doi.org/10.1101/gr.176701.114
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