Difference between revisions of "FlyBase:CRISPR"

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| [http://crispr.mit.edu/ CRISPR Design] ||Identification of gRNA sites genome wide. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. || Zhang Lab<br /> MIT<br /> Boston, MA, USA
 
| [http://crispr.mit.edu/ CRISPR Design] ||Identification of gRNA sites genome wide. Support for multiple species including <em>Drosophila</em> (release 5), zebrafish, mouse, human, and others. || Zhang Lab<br /> MIT<br /> Boston, MA, USA
 
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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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|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

Revision as of 21:56, 5 March 2021

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CRISPR gRNA Design 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
CHOPCHOP Search for gRNA targets. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Configurable options for off-targets, PAM motifs, and 5' requirements. Schier & Church Labs
Harvard University
Cambridge, MA, USA
CRISPR Design Identification of gRNA sites genome wide. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Zhang Lab
MIT
Boston, MA, USA
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
DRSC Find CRISPR 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


CRISPR Stocks

Resource Description Source/Reference
Stocks for Genome Editing Stocks for expression of both Cas9 nuclease and tracrRNA, Guide RNA Stocks (includes the TRiP collections TRIP CRISPR fly stocks and vectors), and CRISPR - UAS-Cas9 & GAL4 (includes the TRiP Toolbox set 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


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). style="background: #efefef;"
MRC Laboratory of Molecular Biology
Cambridge, UK
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
Insect Genomic Technologies Research Coordination Network Discussion and dissemination of advanced technologies for genome modification of insects through symposia, technical workshops, and training fellowships. Institute for Bioscience and Biotechnology Research
University of Maryland
Rockville, MD, 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
DRSC cell-based CRISPR modification Useful references for cell-based CRISPR. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
OXfCRISPR Information about protocols and reagents, new refinements of techniques, useful links to other tools, websites, and discussion groups. Liu lab
University of Oxford
Oxford, UK


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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