Difference between revisions of "FlyBase:CRISPR"
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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 | | [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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| − | |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 | + | |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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| + | | [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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| [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 | | [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="background: #efefef;"| [https:// | + | |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.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 | | [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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| [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 | | [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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| − | |style="background: #efefef;"| [http:// | + | |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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| [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 | | [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 | ||
Latest revision as of 15:32, 27 March 2024
Popular Resource Categories
| All Resources | CRISPR | ScRNA-Seq | RNAi | Stocks | Antibodies | Neuroscience |
| Model Organism Databases |
Images | Maps | Protocols | Papers with 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
- Venken KJ, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. Wiley Interdiscip Rev Dev Biol. 2015 Oct 8. doi: 10.1002/wdev.214. [Epub ahead of print] Review. PubMed PMID: 26447401.
- Gratz1 SJ, Rubinstein CD, Harrison MM, Wildonger J, O'Connor-Giles KM 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. 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. 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.
Selected CRISPR method reports for tissue culture cells
- Bassett AR, Tibbit C, Ponting CP, Liu JL. 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. 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. 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, Knight S, Kanca O, Zirin J, Yang-Zhou D, Hu Y, Rodiger J, Amador G, Bellen HJ, Perrimon N. 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
- Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. 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
- 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. 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
- Huynh N, Depner N, Larson R, King-Jones K. 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. 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. 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. 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). 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 in vivo
- Bassett AR, Tibbit C, Ponting CP, Liu JL. 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. 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. 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. 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
- Huynh N, Depner N, Larson R, King-Jones K. A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila bioRxiv. doi: https://doi.org/10.1101/2020.09.25.314047.
- 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. 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. 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. 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. 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, 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. 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. 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. 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
- 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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