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Here, we describe a set of resources to streamline reporter gene knock-ins in zebrafish and demonstrate the broader utility of the method in mammalian cells. Our approach uses short homology of 24\u201348 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at high frequency at a double strand break in the targeted gene. Our vector series, pGTag (plasmids for Gene Tagging), contains reporters flanked by a universal CRISPR sgRNA sequence which enables in vivo liberation of the homology arms. We observed high rates of germline transmission (22\u2013100%) for targeted knock-ins at eight zebrafish loci and efficient integration at safe harbor loci in porcine and human cells. Our system provides a straightforward and cost-effective approach for high efficiency gene targeting applications in CRISPR and TALEN compatible systems.<\/jats:p>","DOI":"10.7554\/elife.53968","type":"journal-article","created":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T10:04:21Z","timestamp":1589537061000},"source":"Crossref","is-referenced-by-count":150,"title":["Efficient targeted integration directed by short homology in zebrafish and mammalian cells"],"prefix":"10.7554","volume":"9","author":[{"given":"Wesley A","family":"Wierson","sequence":"first","affiliation":[{"name":"Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jordan M","family":"Welker","sequence":"additional","affiliation":[{"name":"Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maira 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