{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T02:48:15Z","timestamp":1774406895615,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T00:00:00Z","timestamp":1602633600000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012728","name":"Frederick National Laboratory for Cancer Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012728","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>With the technology's accessibility and ease of use, CRISPR has been employed widely in many different organisms and experimental settings. As a result, thousands of publications have used CRISPR to make specific genetic perturbations, establishing in itself a resource of validated guide RNA sequences. While numerous computational tools to assist in the design and identification of candidate guide RNAs exist, these are still just at best predictions and generally, researchers inevitably will test multiple sequences for functional activity. Here, we present dbGuide (https:\/\/sgrnascorer.cancer.gov\/dbguide), a database of functionally validated guide RNA sequences for CRISPR\/Cas9-based knockout in human and mouse. Our database not only contains computationally determined candidate guide RNA sequences, but of even greater value, over 4000 sequences which have been functionally validated either through direct amplicon sequencing or manual curation of literature from over 1000 publications. Finally, our established framework will allow for continual addition of newly published and experimentally validated guide RNA sequences for CRISPR\/Cas9-based knockout as well as incorporation of sequences from different gene editing systems, additional species and other types of site-specific functionalities such as base editing, gene activation, repression and epigenetic modification.<\/jats:p>","DOI":"10.1093\/nar\/gkaa848","type":"journal-article","created":{"date-parts":[[2020,9,22]],"date-time":"2020-09-22T07:20:37Z","timestamp":1600759237000},"page":"D871-D876","source":"Crossref","is-referenced-by-count":31,"title":["dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells"],"prefix":"10.1093","volume":"49","author":[{"given":"Alexander A","family":"Gooden","sequence":"first","affiliation":[{"name":"Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA"}]},{"given":"Christine N","family":"Evans","sequence":"additional","affiliation":[{"name":"Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA"}]},{"given":"Timothy P","family":"Sheets","sequence":"additional","affiliation":[{"name":"Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA"}]},{"given":"Michelle E","family":"Clapp","sequence":"additional","affiliation":[{"name":"Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2216-313X","authenticated-orcid":false,"given":"Raj","family":"Chari","sequence":"additional","affiliation":[{"name":"Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,10,13]]},"reference":[{"key":"2021010313113088500_B1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1126\/science.1232033","article-title":"RNA-guided human genome engineering via Cas9","volume":"339","author":"Mali","year":"2013","journal-title":"Science"},{"key":"2021010313113088500_B2","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1126\/science.1231143","article-title":"Multiplex genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2021010313113088500_B3","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s13059-016-1012-2","article-title":"Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR","volume":"17","author":"Haeussler","year":"2016","journal-title":"Genome Biol."},{"key":"2021010313113088500_B4","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nmeth.2812","article-title":"E-CRISP: fast CRISPR target site identification","volume":"11","author":"Heigwer","year":"2014","journal-title":"Nat. Methods"},{"key":"2021010313113088500_B5","doi-asserted-by":"crossref","first-page":"2684","DOI":"10.1093\/bioinformatics\/btaa041","article-title":"Generalizable sgRNA design for improved CRISPR\/Cas9 editing efficiency","volume":"36","author":"Hiranniramol","year":"2020","journal-title":"Bioinformatics"},{"key":"2021010313113088500_B6","doi-asserted-by":"crossref","first-page":"W171","DOI":"10.1093\/nar\/gkz365","article-title":"CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing","volume":"47","author":"Labun","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313113088500_B7","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1093\/bioinformatics\/btv423","article-title":"CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation","volume":"31","author":"Liu","year":"2015","journal-title":"Bioinformatics"},{"key":"2021010313113088500_B8","doi-asserted-by":"crossref","first-page":"4014","DOI":"10.1093\/bioinformatics\/btv537","article-title":"Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites","volume":"31","author":"Park","year":"2015","journal-title":"Bioinformatics"},{"key":"2021010313113088500_B9","doi-asserted-by":"crossref","first-page":"e000033","DOI":"10.1099\/mgen.0.000033","article-title":"EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens","volume":"1","author":"Peng","year":"2015","journal-title":"Microb. Genomics"},{"key":"2021010313113088500_B10","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13062-015-0035-z","article-title":"\u2018Off-Spotter\u2019: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR\/Cas guide RNAs","volume":"10","author":"Pliatsika","year":"2015","journal-title":"Biol. Direct"},{"key":"2021010313113088500_B11","doi-asserted-by":"crossref","first-page":"e0119372","DOI":"10.1371\/journal.pone.0119372","article-title":"CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences","volume":"10","author":"Prykhozhij","year":"2015","journal-title":"PLoS One"},{"key":"2021010313113088500_B12","doi-asserted-by":"crossref","first-page":"e0124633","DOI":"10.1371\/journal.pone.0124633","article-title":"CCTop: an intuitive, flexible and reliable CRISPR\/Cas9 target prediction tool","volume":"10","author":"Stemmer","year":"2015","journal-title":"PLoS One"},{"key":"2021010313113088500_B13","doi-asserted-by":"crossref","first-page":"D822","DOI":"10.1093\/nar\/gkv998","article-title":"CRISPRz: a database of zebrafish validated sgRNAs","volume":"44","author":"Varshney","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313113088500_B14","doi-asserted-by":"crossref","first-page":"4284","DOI":"10.1038\/s41467-019-12281-8","article-title":"Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning","volume":"10","author":"Wang","year":"2019","journal-title":"Nat. Commun."},{"key":"2021010313113088500_B15","doi-asserted-by":"crossref","first-page":"e100448","DOI":"10.1371\/journal.pone.0100448","article-title":"sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites","volume":"9","author":"Xie","year":"2014","journal-title":"PLoS One"},{"key":"2021010313113088500_B16","doi-asserted-by":"crossref","first-page":"e108424","DOI":"10.1371\/journal.pone.0108424","article-title":"CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems","volume":"9","author":"Zhu","year":"2014","journal-title":"PLoS One"},{"key":"2021010313113088500_B17","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1038\/nbt.3437","article-title":"Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9","volume":"34","author":"Doench","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2021010313113088500_B18","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/s41586-018-0686-x","article-title":"Predictable and precise template-free CRISPR editing of pathogenic variants","volume":"563","author":"Shen","year":"2018","journal-title":"Nature"},{"key":"2021010313113088500_B19","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1038\/nbt.3026","article-title":"Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation","volume":"32","author":"Doench","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2021010313113088500_B20","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1038\/nmeth.3047","article-title":"Improved vectors and genome-wide libraries for CRISPR screening","volume":"11","author":"Sanjana","year":"2014","journal-title":"Nat. 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Biol."},{"key":"2021010313113088500_B33","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/nbt.4317","article-title":"Predicting the mutations generated by repair of Cas9-induced double-strand breaks","volume":"37","author":"Allen","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"2021010313113088500_B34","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nbt.3804","article-title":"GuideScan software for improved single and paired CRISPR guide RNA design","volume":"35","author":"Perez","year":"2017","journal-title":"Nat. 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