CLUE: a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries. Issue 13 (1st June 2020)

• Record Type: Journal Article
• Authors: Becker, Martin; Noll-Puchta, Heidi; Amend, Diana; Nolte, Florian; Fuchs, Christiane; Jeremias, Irmela; Braun, Christian J
• Is Part Of: Nucleic acids research. Volume 48:Issue 13(2020)
• Page Start: e78
• Page End: e78
• Publication Date: 2020-06-01
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa459
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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 wet-lab 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 resource-saving approach to produce numerous high quality custom sgRNA libraries in parallel, which will foster their broad use across molecular biosciences.