Difference between revisions of "FlyBase:CRISPR"

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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, 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
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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
 
*  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
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* 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, 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
 
* 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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*  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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* 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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* 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
 
* 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
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* 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
 
* 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
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* 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, 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
 
* 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
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* 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
 
* 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
  

Revision as of 20:47, 5 March 2021

Popular Resource Categories

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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). 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


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