Difference between revisions of "FlyBase:CRISPR"

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=Popular Resource Categories=
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= Popular Resource Categories =
  
 
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|style="text-align: center; padding: 20px;"| <big>[[FlyBase:External_Resources|All Resources]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Antibodies|Antibodies]]</big>
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|style="text-align: center; padding: 15px;"| <big>[[FlyBase:External_Resources|All Resources]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:ScRNA-Seq|ScRNA-Seq]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase: Antibodies|Antibodies]]</big>||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Neuroscience|Neuroscience]]</big>
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|style="text-align: center; padding: 20px;"| <big>[[FlyBase:Model_Organism_Databases|Model Organism<br/> Databases]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Images|Images]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Maps|Maps]]</big> ||style="text-align: center; padding: 20px;"| <big>[http://www.flyrnai.org/tools/protocols/web/ Protocols]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Papers_with_technical_advances|Papers with<br/> Technical Advances]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:GSEA|Gene Set<br/> Enrichment Tools]]</big>
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__TOC__
 
  
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= CRISPR gRNA Design Resources =
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__TOC__
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= CRISPR gRNA Resources =
  
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [http://tools.flycrispr.molbio.wisc.edu/targetFinder/ CRISPR Optimal Target Finder] ||style="background: #efefef;"| Identifies gRNA targets within a provided sequence and additionally searches genome-wide ('''release 6, current FlyBase release''') for potential off-target sites. Includes several <em>Drosophila</em> species.||style="white-space: nowrap; background: #efefef;"|O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
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| [https://cctop.cos.uni-heidelberg.de/index.html CCTop] || CRISPR/Cas9 Target online predictor. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. Notably large set of configurable parameters. || Center for Organismal Studies<br/> University of Heidelberg<br/>Heidelberg, Germany
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|style="white-space: nowrap; background: #efefef;"| [http://targetfinder.flycrispr.neuro.brown.edu/ CRISPR Optimal Target Finder] ||style="background: #efefef;"| Identifies gRNA targets within a provided sequence and additionally searches genome-wide ('''release 6, current FlyBase release''') for potential off-target sites. Includes several <em>Drosophila</em> species.||style="white-space: nowrap; background: #efefef;"|O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
 
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| [http://www.crisprscan.org/ CRISPRscan] || Searchable and browsable collection of genome-wide ('''release 6, current FlyBase release''') sgRNA target sites. Displays sgRNA sites as tracks on UCSC's genome browser and allows searching via gene or prediction via sequence. Support for multiple species (fly, zebrafish, mouse, human, others).|| Giraldez Lab<br /> Yale University<br /> New Haven, CT, USA
 
| [http://www.crisprscan.org/ CRISPRscan] || Searchable and browsable collection of genome-wide ('''release 6, current FlyBase release''') sgRNA target sites. Displays sgRNA sites as tracks on UCSC's genome browser and allows searching via gene or prediction via sequence. Support for multiple species (fly, zebrafish, mouse, human, others).|| Giraldez Lab<br /> Yale University<br /> New Haven, CT, USA
 
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|style="background: #efefef;"|[http://www.flyrnai.org/crispr2/ DRSC Find CRISPR Tool] ||style="background: #efefef;"| A tool for discovering gRNA targets located throughout the fly genome (release 5). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets.  ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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|style="background: #efefef;"| [https://dgrc.bio.indiana.edu/gRNA DGRC sgRNA libraries] ||style="background: #efefef;"| Guide RNA collections available from the Drosophila Genomics Resource Center (DGRC) ||style="background: #efefef;"| Indiana University<br/> Bloomington, IN, USA
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| [http://cas9.cbi.pku.edu.cn/ Cas9 Design] || A CRISPR/Cas9 guide RNA design tool. Support for multiple species including fly (release 5), zebrafish, mouse, human, and others. || Center for Bioinformatics<br/> Peking University<br/> Beijing, China
 
 
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|style="background: #efefef;"| [http://crispr.cos.uni-heidelberg.de/ CCTop] ||style="background: #efefef;"| CRISPR/Cas9 Target online predictor. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others.  ||style="background: #efefef;"| Center for Organismal Studies<br/> University of Heidelberg<br/>Heidelberg, Germany
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| [https://www.flyrnai.org/crispr3/web/ DRSC Find CRISPRs Tool] || A tool for discovering gRNA targets located throughout the fly genome ('''release 6, current FlyBase release'''). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets.  ||style="white-space: nowrap;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
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| [http://www.e-crisp.org/E-CRISP/designcrispr.html E-CRISP] || gRNA genome-wide target finder, searchable via  gene symbol or sequence. Support for multiple species. ||Boutros lab, DKFZ<br/> Heidelberg, Germany
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|style="background: #efefef;"| [http://www.e-crisp.org/E-CRISP/designcrispr.html E-CRISP] ||style="background: #efefef;"| gRNA genome-wide target finder, searchable via  gene symbol or sequence. Relaxed, "medium", or strict search options. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. ||style="background: #efefef;"| Boutros Lab, DKFZ<br/> Heidelberg, Germany
 
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|style="background: #efefef;"| [https://chopchop.rc.fas.harvard.edu/ CHOPCHOP] ||style="background: #efefef;"| Search for gRNA targets (release 5). ||style="background: #efefef;"| Schier & Church Labs<br /> Harvard University<br /> Cambridge, MA, USA
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| [https://platinum-crispr.bham.ac.uk/predict.pl PlatinumCRISPr] || gRNA target finder. Incorporates correct sgRNA folding, various sequence elements and sgRNA/Cas9 structural features to predict high cleavage efficiency. Also allows separate crRNA and tracrRNA folding analysis. Applicable to any organism. || Soller Lab, School of Biosciences<br/>Arnold Lab, Institute of Cancer and Genome Sciences<br/> University of Birmingham<br/>Birmingham, UK
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| [http://crispr.mit.edu/ CRISPR Design] ||Identification of gRNA sites genome wide (release 5). Offers options for multiple species. || Zhang Lab<br /> MIT<br /> Boston, MA, USA
 
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|style="background: #efefef;"| [http://tefor.net/crispor/crispor.cgi CRISPOR] ||style="background: #efefef;"| A program that helps design, evaluate, and clone guide sequences for the CRISPR/Cas9 system. Allows for searches across multiple species of <em>Drosophila</em>, including melanogaster (release 5).||style="background: #efefef;"| Tefor<br />France
 
 
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= CRISPR Stocks =
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= CRISPR Stocks and Cell Lines=
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Source/Reference
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| [https://bdsc.indiana.edu/stocks/genome_editing/index.html Stocks for Genome Editing] || Stocks for expression of both Cas9 nuclease and tracrRNA, Guide RNA Stocks (includes the [https://fgr.hms.harvard.edu/crispr-fly-stocks-and-vectors TRiP collections]), and CRISPR - UAS-Cas9 & GAL4 (includes the  [https://fgr.hms.harvard.edu/trip-crispr-toolbox-fly-stocks TRIP-CRISPR Toolbox set])}. ||style="white-space: nowrap;"| Bloomington Drosophila Stock Center (BDSC)<br/> Indiana University<br/> Bloomington, IN, USA
 
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|style="white-space: nowrap; background: #efefef;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef;"| The Bloomington Stock Center's CRISPR/Cas9 page. Includes various stocks for expression of both Cas9 and tracrRNA. ||style="background: #efefef;"| Bloomington Drosophila Stock Center (BDSC)<br/> Indiana University<br/> Bloomington, IN, USA
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|style="background: #efefef;"| [https://shop.vbc.ac.at/vdrc_store/hd-info Heidelberg CFD CRISPR Library Stocks] ||style="background: #efefef;"| This library, for tissue specific CRISPR mutagenesis, was created by the laboratory of Michael Boutros at the DKFZ (see [http://www.crisprflydesign.org CRISPR fly design]) and donated to the [https://shop.vbc.ac.at/vdrc_store/ VDRC] for distribution ||style="background: #efefef;" | <br/> DKFZ<br/> Heidelberg, Germany
 
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| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || Information on stocks generated by the CRISPR Fly Design group at the MRC Laboratory of Molecular Biology.  ||style="white-space: nowrap;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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| [http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG-FLY CRISPR/Cas9] || Reagents, protocols, and online tools developed for genome engineering in <em>Drosophila</em>.  ||style="white-space: nowrap;"| NIG-FLY<br/> National Institute of Genetics<br/> Mishima, Japan
 
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|style="background: #efefef;"| [http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG-FLY CRISPR/Cas9] ||style="background: #efefef;"| Reagents, protocols, and online tools developed for genome engineering in <em>Drosophila</em> ||style="background: #efefef;"| NIG-FLY<br/> National Institute of Genetics<br/> Mishima, Japan
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|style="background: #efefef;"| [https://dgrc.bio.indiana.edu/Search?category=&query=crispr DGRC CRISPR Cell Lines] ||style="background: #efefef;"| A catalog of CRISPR Cell lines at the Drosophila Genomics Resource Center (DGRC) ||style="background: #efefef;"|Indiana University<br/> Bloomington, IN, USA
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [https://www.addgene.org/crispr/drosophila/ Addgene CRISPR/Cas9 Plasmids for use in insects]||style="white-space: nowrap; background: #efefef;"| A list of available Cas9 & gRNA expression plasmids for use in insects, including <em>Drosophila</em>. ||style="background: #efefef;"| Addgene<br />Cambridge, MA, USA
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| [https://www.addgene.org/crispr/drosophila/ Addgene CRISPR/Cas9 Plasmids for use in insects] || A list of available Cas9 & gRNA expression plasmids for use in insects, including <em>Drosophila</em>. ||style="white-space: nowrap;"| Addgene<br />Cambridge, MA, USA
 
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| [http://www.crisprflydesign.org/plasmids/ CRISPR Fly Design Plasmids] || Descriptions and information regarding the plasmids created by the CRISPR Fly Design group (also [http://www.addgene.org/search/advanced/?q=Bullock#p=true deposited at Addgene]). || MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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|style="background: #efefef;"| [http://crisprflydesign.org/ CRISPR Fly Design Plasmids] ||style="background: #efefef;"| Descriptions and information regarding the plasmids created by the CRISPR Fly Design group (also [http://www.addgene.org/search/advanced/?q=Bullock#p=true deposited at Addgene]). ||style="background: #efefef;"|<br/> MRC Laboratory of Molecular Biology<br /> Cambridge, UK
 
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|style="background: #efefef;"| [http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG-FLY CRISPR/Cas9] ||style="background: #efefef;"| Reagents, protocols, and online tools developed for genome engineering in <em>Drosophila</em> ||style="background: #efefef;"| NIG-FLY<br/> National Institute of Genetics<br/> Mishima, Japan
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| [https://dgrc.bio.indiana.edu/Search?category=&query=crispr DGRC CRISPR Vectors] || A catalog of useful CRISPR vectors available from the Drosophila Genomics Resource Center (DGRC)  ||style="white-space: nowrap;"| Inidana University<br/> Bloomington, IN, USA
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|style="background: #efefef;"| [http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG-FLY CRISPR/Cas9] ||style="background: #efefef;"| Reagents, protocols, and online tools developed for genome engineering in <em>Drosophila</em>. ||style="background: #efefef;"| NIG-FLY<br/> National Institute of Genetics<br/> Mishima, Japan
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [http://www.crisprflydesign.org/ CRISPR Fly Design]||style="white-space: nowrap; background: #efefef;"| An overview and resource collection for CRISPR gene editing in <em>Drosophila</em>. ||style="background: #efefef;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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| [https://crispresso.pinellolab.partners.org/submission CRISPRESSO2] || Analysis of genome editing outcomes from deep sequencing data  ||style="white-space: nowrap;"| Broad Institute, Massachusetts General Hospital, Harvard Medical School,<br /> Children's Hospital, Dana Farber Cancer Institute<br /> Cambridge, MA<br /> Boston, MA
 
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| [http://flycrispr.molbio.wisc.edu/ flyCRISPR] || An overview and resource collection for CRISPR gene editing in <em>Drosophila</em>. || O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
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|style="white-space: nowrap; background: #efefef;"| [https://www.crisprflydesign.org// CRISPR Fly Design]||style="white-space: nowrap; background: #efefef;"| Reagents, protocols, and results from fly CRISPR/Cas9 experiments. ||style="background: #efefef;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
 
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| style="background: #efefef;"| [http://igtrcn.org/ Insect Genomic Technologies Research Coordination Network] || style="background: #efefef;"| Discussion and dissemination of advanced technologies for genome modification of insects through symposia, technical workshops, and training fellowships. || style="background: #efefef; white-space: nowrap;"|Institute for Bioscience and Biotechnology Research<br />University of Maryland<br />Rockville, MD, USA
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| [https://flycrispr.org/ flyCRISPR] || An overview and resource collection for CRISPR gene editing in <em>Drosophila</em>. || O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
 
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| [http://flyrnai.blogspot.com/search/label/CRISPRs FlyRNAi Blog, CRISPR tags] || A research blog tracking functional genomics techniques in <em>Drosophila</em>, filtered for keyword: CRISPRs. || Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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|style="background: #efefef;"| [https://fgr.hms.harvard.edu/publications/technology/fly-cell-based-crispr DRSC cell-based CRISPR modification] ||style="background: #efefef;"| Useful references for cell-based CRISPR. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
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|style="background: #efefef;"| [http://www.flyrnai.org/DRSC-Protocol_single_cell_cloning.html DRSC Single Cell Cloning Protocol] ||style="background: #efefef;"| Single-cell cloning method useful for <em>Drosophila</em> cell CRISPR gene editing. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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| [https://fgr.hms.harvard.edu/crispr-fly-stocks-and-vectors TRiP CRISPR fly stock information] || Links and descriptions for TRiP-CRISPR overexpression stocks, TRiP-CRISPR knockout stocks, and TRiP-CRISPR toolbox stocks || Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
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|[http://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr OXfCRISPR] ||Information about protocols and reagents, new refinements of techniques, useful links to other tools, websites, and discussion groups. || Liu lab<br/> University of Oxford<br/> Oxford, UK
 
 
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= Selected recent CRISPR method reviews =
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= Selected CRISPR method reviews =
  
 
*  Venken KJ, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. [http://www.ncbi.nlm.nih.gov/pubmed/26447401 '''Genome engineering: Drosophila melanogaster and beyond.'''] Wiley Interdiscip Rev Dev Biol. 2015 Oct 8. doi: 10.1002/wdev.214. [Epub ahead of print<nowiki>]</nowiki> Review. PubMed PMID: 26447401.
 
*  Venken KJ, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. [http://www.ncbi.nlm.nih.gov/pubmed/26447401 '''Genome engineering: Drosophila melanogaster and beyond.'''] Wiley Interdiscip Rev Dev Biol. 2015 Oct 8. doi: 10.1002/wdev.214. [Epub ahead of print<nowiki>]</nowiki> Review. PubMed PMID: 26447401.
 +
* Gratz1 SJ, Rubinstein CD, Harrison MM, Wildonger J, O'Connor-Giles KM [http://onlinelibrary.wiley.com/doi/10.1002/0471142727.mb3102s111/full '''CRISPR-Cas9 Genome Editing in Drosophila'''] Curr Protoc Mol Biol. 2015 Jul 1;111:31.2.1-31.2.20. doi: 10.1002/0471142727.mb3102s111. PMID: 26131852; PMCID: PMC4506758.
 
*  Beumer KJ, Carroll D. [http://www.ncbi.nlm.nih.gov/pubmed/24412316 '''Targeted genome engineering techniques in Drosophila.'''] Methods. 2014 Jun 15;68(1):29-37. doi: 10.1016/j.ymeth.2013.12.002. Epub 2014 Jan 8. Review. PubMed PMID: 24412316; PubMed Central PMCID: PMC4048800.
 
*  Beumer KJ, Carroll D. [http://www.ncbi.nlm.nih.gov/pubmed/24412316 '''Targeted genome engineering techniques in Drosophila.'''] Methods. 2014 Jun 15;68(1):29-37. doi: 10.1016/j.ymeth.2013.12.002. Epub 2014 Jan 8. Review. PubMed PMID: 24412316; PubMed Central PMCID: PMC4048800.
 
*  Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25953352 '''A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila. J Genet Genomics.'''] 2015 Apr 20;42(4):141-9. doi: 10.1016/j.jgg.2015.02.007. Epub 2015 Mar 12. Review. PubMed PMID: 25953352.
 
*  Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25953352 '''A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila. J Genet Genomics.'''] 2015 Apr 20;42(4):141-9. doi: 10.1016/j.jgg.2015.02.007. Epub 2015 Mar 12. Review. PubMed PMID: 25953352.
  
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= Selected recent CRISPR method reports for tissue culture cells =
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= Selected CRISPR method reports for tissue culture cells =
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 +
*  Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24326186 '''Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9.'''] Biol Open. 2014 Jan 15;3(1):42-9. doi: 10.1242/bio.20137120. PMID: 24326186
 +
 
 +
*  Bassett AR, Kong L, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells.'''] J Genet Genomics. 2015 Jun 20;42(6):301-9. doi: 10.1016/j.jgg.2015.03.011. Epub 2015 Apr 18. PMID: 26165496
 +
 
 +
* Bosch JA, Colbeth, R, Zirin, J, Perrimon, N. [http://www.ncbi.nlm.nih.gov/pubmed/31685521 '''Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids..'''] Genetics 214(1): 75--89. doi: 10.1534/genetics.119.302819. PMID: 31685521
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 +
* Bosch JA, Knight S, Kanca O, Zirin J, Yang-Zhou D, Hu Y, Rodiger J, Amador G, Bellen HJ, Perrimon N. [https://pubmed.ncbi.nlm.nih.gov/31869524/ Use of the CRISPR-Cas9 System in Drosophila Cultured Cells to Introduce Fluorescent Tags into Endogenous Genes] Curr Protoc Mol Biol. 2020 Mar;130(1):e112. doi: 10.1002/cpmb.112. PMID: 31869524
  
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*  Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24326186 '''Mutagenesis and homologous recombination in Drosophila cell lines using CRISPR/Cas9.'''] Biol Open. 2014 Jan 15;3(1):42-9. doi: 10.1242/bio.20137120. PMID: 24326186.
 
 
*  Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells.'''] Nucleic Acids Res. 2014 Jun;42(11):e89. doi: 10.1093/nar/gku289. Epub 2014 Apr 19. PMID: 24748663
 
*  Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells.'''] Nucleic Acids Res. 2014 Jun;42(11):e89. doi: 10.1093/nar/gku289. Epub 2014 Apr 19. PMID: 24748663
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*  Bassett AR, Kong L, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/24748663 '''A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells.'''] J Genet Genomics. 2015 Jun 20;42(6):301-9. doi: 10.1016/j.jgg.2015.03.011. Epub 2015 Apr 18. PMID: 26165496
+
 
 
* Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N. [http://www.ncbi.nlm.nih.gov/pubmed/26350902 '''Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi.'''] Sci Signal. 2015 Sep 8;8(393):rs9. doi: 10.1126/scisignal.aab3729. PMID: 26350902
 
* Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, Lin S, Buckner M, Tao R, Yilmazel B, Mohr SE, Manning BD, Perrimon N. [http://www.ncbi.nlm.nih.gov/pubmed/26350902 '''Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi.'''] Sci Signal. 2015 Sep 8;8(393):rs9. doi: 10.1126/scisignal.aab3729. PMID: 26350902
  
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= Selected recent CRISPR method reports for <em>in vivo</em> =
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* Huynh N, Depner N, Larson R, King-Jones K. [https://www.biorxiv.org/content/10.1101/2020.09.25.314047v1 A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila] bioRxiv. doi: https://doi.org/10.1101/2020.09.25.314047
 +
 
 +
* Kunzelmann S, Böttcher R, Schmidts I, Förstemann K. [http://www.g3journal.org/content/early/2016/04/11/g3.116.028241.abstract?papetoc '''A comprehensive toolbox for genome editing in cultured Drosophila cells.'''] G3 (Bethesda). 2016 Apr 13; doi:10.1534/g3.116.028241
 +
 
 +
* Viswanatha R, Brathwaite R, Hu Y, Li Z, Rodiger J, Merckaert P, Chung V, Mohr SE, Perrimon N. [https://pubmed.ncbi.nlm.nih.gov/31763777/ Pooled CRISPR Screens in Drosophila Cells] Curr Protoc Mol Biol. 2019 Dec;129(1):e111. doi: 10.1002/cpmb.111. PMID: 31763777
 +
 
 +
* Viswanatha, R, Zaffagni, M, Zirin, J, Perrimon, N, Kadener, S. [https://www.biorxiv.org/content/10.1101/2020.11.01.364166v1 '''CRISPR-Cas13 mediated Knock Down in Drosophila cultured cells'''] bioRxiv. doi: https://doi.org/10.1101/2020.11.01.364166
 +
 
 +
* Xia, B, Amador, G, Viswanatha, R, Zirin, J, Mohr, SE, Perrimon, N. (2020). [https://pubmed.ncbi.nlm.nih.gov/32958931/ CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells.]  Nat. Protoc., 21 Sept. 2020 15(10): 3478-3498. doi:10.1038/s41596-020-0383-8  PubMed PMID: 32958931
 +
 
 +
= Selected CRISPR method reports for <em>in vivo</em> =
 +
 
 +
* Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/23827738 '''Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.'''] Cell Rep. 2013 Jul 11;4(1):220-8. doi: 10.1016/j.celrep.2013.06.020. Epub 2013 Jul 1. PMID: 23827738
 +
 
 +
* Bosch JA, Colbeth, R, Zirin, J, Perrimon, N. [http://www.ncbi.nlm.nih.gov/pubmed/31685521 '''Gene Knock-Ins in Drosophila Using Homology-Independent Insertion of Universal Donor Plasmids..'''] Genetics 214(1): 75--89. doi: 10.1534/genetics.119.302819. PMID: 31685521
 +
 
 +
* Bosch JA, Birchak, G, Perrimon, N. [http://www.ncbi.nlm.nih.gov/pubmed/33443210 '''Precise genome engineering in Drosophila using prime editing.'''] Proc. Natl. Acad. Sci. U.S.A. 118(1): e2021996118. doi: 10.1073/pnas.2021996118. PMID: 33443210
 +
 
 
* Gratz SJ, Cummings AM, Nguyen JN, Hamm DC, Donohue LK, Harrison MM, Wildonger J, O'Connor-Giles KM. [http://www.ncbi.nlm.nih.gov/pubmed/23709638 '''Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease.'''] Genetics. 2013 Aug;194(4):1029-35. doi: 10.1534/genetics.113.152710. Epub 2013 May 24. PMID: 23709638
 
* Gratz SJ, Cummings AM, Nguyen JN, Hamm DC, Donohue LK, Harrison MM, Wildonger J, O'Connor-Giles KM. [http://www.ncbi.nlm.nih.gov/pubmed/23709638 '''Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease.'''] Genetics. 2013 Aug;194(4):1029-35. doi: 10.1534/genetics.113.152710. Epub 2013 May 24. PMID: 23709638
  
−
* Bassett AR, Tibbit C, Ponting CP, Liu JL. [http://www.ncbi.nlm.nih.gov/pubmed/23827738 '''Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.'''] Cell Rep. 2013 Jul 11;4(1):220-8. doi: 10.1016/j.celrep.2013.06.020. Epub 2013 Jul 1. PMID: 23827738
+
* Huynh N, Depner N, Larson R, King-Jones K. [https://www.biorxiv.org/content/10.1101/2020.09.25.314047v1 A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila] bioRxiv. doi: https://doi.org/10.1101/2020.09.25.314047.
  
−
* Yu Z, Ren M, Wang Z, Zhang B, Rong YS, Jiao R, Gao G. [http://www.ncbi.nlm.nih.gov/pubmed/23833182 '''Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila.'''] Genetics. 2013 Sep;195(1):289-91. doi: 10.1534/genetics.113.153825. Epub 2013 Jul 5. PMID: 23833182
+
* Kanca O, Zirin J, Garcia-Marques J, Knight SM, Yang-Zhou D, Amador G, Chung H, Zuo Z, Ma L, He Y, Lin WW, Fang Y, Ge M, Yamamoto S, Schulze K, Hu Y, Spradling AC, Mohr SE, Perrimon N, Bellen HJ. [https://pubmed.ncbi.nlm.nih.gov/31674908/ An efficient CRISPR-based strategy to insert small and large fragments of DNA using short homology arms] Elife. 2019 Nov 1;8:e51539. doi: 10.7554/eLife.51539. PMID: 31674908
  
 
* Kondo S, Ueda R. [http://www.ncbi.nlm.nih.gov/pubmed/24002648 '''Highly improved gene targeting by germline-specific Cas9 expression in Drosophila.'''] Genetics. 2013 Nov;195(3):715-21. doi: 10.1534/genetics.113.156737. Epub 2013 Sep 3. PMID: 24002648
 
* Kondo S, Ueda R. [http://www.ncbi.nlm.nih.gov/pubmed/24002648 '''Highly improved gene targeting by germline-specific Cas9 expression in Drosophila.'''] Genetics. 2013 Nov;195(3):715-21. doi: 10.1534/genetics.113.156737. Epub 2013 Sep 3. PMID: 24002648
 +
 +
* Port F, Muschalik N, Bullock SL. [http://www.ncbi.nlm.nih.gov/pubmed/25999583 '''Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research.'''] G3 (Bethesda). 2015 May 20;5(7):1493-502. doi: 10.1534/g3.115.019083. PMID: 25999583
  
 
* Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J, Perrimon N, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/24191015 '''Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9.'''] Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19012-7. doi: 10.1073/pnas.1318481110. Epub 2013 Nov 4. PMID: 24191015
 
* Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu LP, Yang Z, Mao D, Sun L, Wu Q, Ji JY, Xi J, Mohr SE, Xu J, Perrimon N, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/24191015 '''Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9.'''] Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19012-7. doi: 10.1073/pnas.1318481110. Epub 2013 Nov 4. PMID: 24191015
  
−
* Port F, Muschalik N, Bullock SL. [http://www.ncbi.nlm.nih.gov/pubmed/25999583 '''Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research.'''] G3 (Bethesda). 2015 May 20;5(7):1493-502. doi: 10.1534/g3.115.019083. PMID: 25999583
+
* Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25437567 '''Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila.'''] Cell Rep. 2014 Nov 6;9(3):1151-62. doi: 10.1016/j.celrep.2014.09.044. Epub 2014 Oct 23. PMID: 25437567
 +
 
 +
* Viswanatha, R, Zaffagni, M, Zirin, J, Perrimon, N, Kadener, S. [https://www.biorxiv.org/content/10.1101/2020.11.01.364166v1 '''CRISPR-Cas13 mediated Knock Down in Drosophila cultured cells'''] bioRxiv. doi: https://doi.org/10.1101/2020.11.01.364166
 +
 
 +
* Yu Z, Ren M, Wang Z, Zhang B, Rong YS, Jiao R, Gao G. [http://www.ncbi.nlm.nih.gov/pubmed/23833182 '''Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila.'''] Genetics. 2013 Sep;195(1):289-91. doi: 10.1534/genetics.113.153825. Epub 2013 Jul 5. PMID: 23833182
  
−
* Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, Yang SJ, Qiao HH, Wang X, Hu Q, Deng P, Liu LP, Ji JY, Li JB, Ni JQ. [http://www.ncbi.nlm.nih.gov/pubmed/25437567 '''Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila.'''] Cell Rep. 2014 Nov 6;9(3):1151-62. doi: 10.1016/j.celrep.2014.09.044. Epub 2014 Oct 23. PMID: 25437567
+
* Zirin J, Hu Y, Liu L, Yang-Zhou D, Colbeth R, Yan D, Ewen-Campen B, Tao R, Vogt E, VanNest S, Cavers C, Villalta C, Comjean A, Sun J, Wang X, Jia Y, Zhu R, Peng P, Yu J, Shen D, Qiu Y, Ayisi L, Ragoowansi H, Fenton E, Efrem S, Parks A, Saito K, Kondo S, Perkins L, Mohr SE, Ni J, Perrimon N. [https://pubmed.ncbi.nlm.nih.gov/32071193/ Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies] Genetics. 2020 Apr;214(4):755-767. doi: 10.1534/genetics.119.302964. Epub 2020 Feb 18. PMID: 32071193
 
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&nbsp; [[#top|Back to top.]] | [[FlyBase:External_Resources|Back to All Resources Page.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
  
 
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Latest revision as of 15:32, 27 March 2024

Popular Resource Categories

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Technical Advances		 Gene Set
Enrichment Tools


CRISPR gRNA Resources

Resource Description Author/Source
CCTop CRISPR/Cas9 Target online predictor. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Notably large set of configurable parameters. Center for Organismal Studies
University of Heidelberg
Heidelberg, Germany
CRISPR Optimal Target Finder Identifies gRNA targets within a provided sequence and additionally searches genome-wide (release 6, current FlyBase release) for potential off-target sites. Includes several Drosophila species. O'Connor-Giles, Wildonger, and Harrison Labs
University of Wisconsin-Madison
WI, USA
CRISPRscan Searchable and browsable collection of genome-wide (release 6, current FlyBase release) sgRNA target sites. Displays sgRNA sites as tracks on UCSC's genome browser and allows searching via gene or prediction via sequence. Support for multiple species (fly, zebrafish, mouse, human, others). Giraldez Lab
Yale University
New Haven, CT, USA
DGRC sgRNA libraries Guide RNA collections available from the Drosophila Genomics Resource Center (DGRC) Indiana University
Bloomington, IN, USA
DRSC Find CRISPRs Tool A tool for discovering gRNA targets located throughout the fly genome (release 6, current FlyBase release). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
E-CRISP gRNA genome-wide target finder, searchable via gene symbol or sequence. Relaxed, "medium", or strict search options. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Boutros Lab, DKFZ
Heidelberg, Germany
PlatinumCRISPr gRNA target finder. Incorporates correct sgRNA folding, various sequence elements and sgRNA/Cas9 structural features to predict high cleavage efficiency. Also allows separate crRNA and tracrRNA folding analysis. Applicable to any organism. Soller Lab, School of Biosciences
Arnold Lab, Institute of Cancer and Genome Sciences
University of Birmingham
Birmingham, UK


CRISPR Stocks and Cell Lines

Resource Description Source/Reference
Stocks for Genome Editing Stocks for expression of both Cas9 nuclease and tracrRNA, Guide RNA Stocks (includes the TRiP collections), and CRISPR - UAS-Cas9 & GAL4 (includes the TRIP-CRISPR Toolbox set)}. Bloomington Drosophila Stock Center (BDSC)
Indiana University
Bloomington, IN, USA
Heidelberg CFD CRISPR Library Stocks This library, for tissue specific CRISPR mutagenesis, was created by the laboratory of Michael Boutros at the DKFZ (see CRISPR fly design) and donated to the VDRC for distribution
DKFZ
Heidelberg, Germany
NIG-FLY CRISPR/Cas9 Reagents, protocols, and online tools developed for genome engineering in Drosophila. NIG-FLY
National Institute of Genetics
Mishima, Japan
DGRC CRISPR Cell Lines A catalog of CRISPR Cell lines at the Drosophila Genomics Resource Center (DGRC) Indiana University
Bloomington, IN, USA


CRISPR Vectors

Resource Description Author/Source
Addgene CRISPR/Cas9 Plasmids for use in insects A list of available Cas9 & gRNA expression plasmids for use in insects, including Drosophila. Addgene
Cambridge, MA, USA
CRISPR Fly Design Plasmids Descriptions and information regarding the plasmids created by the CRISPR Fly Design group (also deposited at Addgene).
MRC Laboratory of Molecular Biology
Cambridge, UK
DGRC CRISPR Vectors A catalog of useful CRISPR vectors available from the Drosophila Genomics Resource Center (DGRC) Inidana University
Bloomington, IN, USA
NIG-FLY CRISPR/Cas9 Reagents, protocols, and online tools developed for genome engineering in Drosophila. NIG-FLY
National Institute of Genetics
Mishima, Japan


Additional Useful CRISPR Links

Resource Description Author/Source
CRISPRESSO2 Analysis of genome editing outcomes from deep sequencing data Broad Institute, Massachusetts General Hospital, Harvard Medical School,
Children's Hospital, Dana Farber Cancer Institute
Cambridge, MA
Boston, MA
CRISPR Fly Design Reagents, protocols, and results from fly CRISPR/Cas9 experiments. MRC Laboratory of Molecular Biology
Cambridge, UK
flyCRISPR An overview and resource collection for CRISPR gene editing in Drosophila. O'Connor-Giles, Wildonger, and Harrison Labs
University of Wisconsin-Madison
WI, USA
DRSC cell-based CRISPR modification Useful references for cell-based CRISPR. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
TRiP CRISPR fly stock information Links and descriptions for TRiP-CRISPR overexpression stocks, TRiP-CRISPR knockout stocks, and TRiP-CRISPR toolbox stocks Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA


Selected CRISPR method reviews

Selected CRISPR method reports for tissue culture cells

  • Viswanatha R, Brathwaite R, Hu Y, Li Z, Rodiger J, Merckaert P, Chung V, Mohr SE, Perrimon N. Pooled CRISPR Screens in Drosophila Cells Curr Protoc Mol Biol. 2019 Dec;129(1):e111. doi: 10.1002/cpmb.111. PMID: 31763777

Selected CRISPR method reports for in vivo

  • Zirin J, Hu Y, Liu L, Yang-Zhou D, Colbeth R, Yan D, Ewen-Campen B, Tao R, Vogt E, VanNest S, Cavers C, Villalta C, Comjean A, Sun J, Wang X, Jia Y, Zhu R, Peng P, Yu J, Shen D, Qiu Y, Ayisi L, Ragoowansi H, Fenton E, Efrem S, Parks A, Saito K, Kondo S, Perkins L, Mohr SE, Ni J, Perrimon N. Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies Genetics. 2020 Apr;214(4):755-767. doi: 10.1534/genetics.119.302964. Epub 2020 Feb 18. PMID: 32071193


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