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Becker, M. ; Noll-Puchta, H.* ; Amend, D. ; Nolte, F.* ; Fuchs, C. ; Jeremias, I. ; Braun, C.J.*

CLUE: A bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries.

Nucleic Acids Res. 48:e78 (2020)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
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The systematic perturbation of genomes using CRISPR/Cas9 deciphers gene function at an unprecedented rate, depth and ease. Commercially available sgRNA libraries typically contain tens of thousands of pre-defined constructs, resulting in a complexity challenging to handle. In contrast, custom sgRNA libraries comprise gene sets of self-defined content and size, facilitating experiments under complex conditions such as in vivo systems. To streamline and upscale cloning of custom libraries, we present CLUE, a bioinformatic and wetlab pipeline for the multiplexed generation of pooled sgRNA libraries. CLUE starts from lists of genes or pasted sequences provided by the user and designs a single synthetic oligonucleotide pool containing various libraries. At the core of the approach, a barcoding strategy for unique primer binding sites allows amplifying different user-defined libraries from one single oligonucleotide pool. We prove the approach to be straightforward, versatile and specific, yielding uniform sgRNA distributions in all resulting libraries, virtually devoid of cross-contaminations. For in silico library multiplexing and design, we established an easy-to-use online platform at www. crispr-clue.de. All in all, CLUE represents a resourcesaving approach to produce numerous high quality custom sgRNA libraries in parallel, which will foster their broad use across molecular biosciences.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Scale Crispr-cas9 Knockout; Genomic Dna; Tumorigenesis; Targets; Genes; Base
Language english
Publication Year 2020
HGF-reported in Year 2020
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Journal Nucleic Acids Research
Quellenangaben Volume: 48, Issue: 13, Pages: , Article Number: e78 Supplement: ,
Publisher Oxford University Press
Publishing Place Great Clarendon St, Oxford Ox2 6dp, England
Reviewing status Peer reviewed
Institute(s) Research Unit Apoptosis in Hematopoietic Stem Cells (AHS)
Institute of Computational Biology (ICB)
POF-Topic(s) 30204 - Cell Programming and Repair
30205 - Bioengineering and Digital Health
Research field(s) Stem Cell and Neuroscience
Enabling and Novel Technologies
PSP Element(s) G-506600-001
G-503800-001
Grants Dr Helmut Legerlotz Stiftung
Care for Rare Foundation
Beug Foundation for Metastasis Research
Society for the Advancement of Science and Research of the LMU Medical Faculty (WiFoMed)
European Research Council
Mildred Scheel Professorship by German Cancer Aid
German Research Foundation (DFG) Collaborative Research Center 1243 `Genetic and Epigenetic Evolution of Hematopoietic Neoplasms'
DFG
Bettina Brau Stiftung
Max-Eder Program of Deutsche Krebshilfe
DOI 10.1093/nar/gkaa459
WOS ID WOS:000574293400006
Scopus ID 85088496052
PubMed ID 32479629
Erfassungsdatum 2020-06-03
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