CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries

BACKGROUND: Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. RESULTS: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated g...

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Autores principales: Heigwer, Florian, Zhan, Tianzuo, Breinig, Marco, Winter, Jan, Brügemann, Dirk, Leible, Svenja, Boutros, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807595/
https://www.ncbi.nlm.nih.gov/pubmed/27013184
http://dx.doi.org/10.1186/s13059-016-0915-2
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author Heigwer, Florian
Zhan, Tianzuo
Breinig, Marco
Winter, Jan
Brügemann, Dirk
Leible, Svenja
Boutros, Michael
author_facet Heigwer, Florian
Zhan, Tianzuo
Breinig, Marco
Winter, Jan
Brügemann, Dirk
Leible, Svenja
Boutros, Michael
author_sort Heigwer, Florian
collection PubMed
description BACKGROUND: Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. RESULTS: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CONCLUSION: CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0915-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-48075952016-03-25 CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries Heigwer, Florian Zhan, Tianzuo Breinig, Marco Winter, Jan Brügemann, Dirk Leible, Svenja Boutros, Michael Genome Biol Software BACKGROUND: Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. RESULTS: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. To demonstrate its utility, we perform a pooled screen for modulators of the TNF-related apoptosis inducing ligand (TRAIL) pathway using a custom library of 12,471 sgRNAs. CONCLUSION: CLD predicts a high fraction of functional sgRNAs and is publicly available at https://github.com/boutroslab/cld. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0915-2) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-24 /pmc/articles/PMC4807595/ /pubmed/27013184 http://dx.doi.org/10.1186/s13059-016-0915-2 Text en © Heigwer et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Heigwer, Florian
Zhan, Tianzuo
Breinig, Marco
Winter, Jan
Brügemann, Dirk
Leible, Svenja
Boutros, Michael
CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title_full CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title_fullStr CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title_full_unstemmed CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title_short CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
title_sort crispr library designer (cld): software for multispecies design of single guide rna libraries
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807595/
https://www.ncbi.nlm.nih.gov/pubmed/27013184
http://dx.doi.org/10.1186/s13059-016-0915-2
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