Difference between revisions of "FlyBase:Images"

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This image-based resources page has been generously contributed by [https://www.mpi-cbg.de/research-groups/current-groups/pavel-tomancak/research-focus/ Pavel Tomancak] of the Max Planck Institute of Molecular Cell Biology and Genetics.
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This image-based resources page has been generously contributed by [https://www.mpi-cbg.de/research-groups/current-groups/pavel-tomancak/research-focus/ '''Pavel Tomancak'''] of the Max Planck Institute of Molecular Cell Biology and Genetics.
  
 
= Imaged Based Resources =
 
= Imaged Based Resources =
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= Tools for Image Visualization and Annotation =
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= CRISPR Vectors =
  
 
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
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|style="white-space: nowrap; background: #efefef;"| [http://catmaid.org CATMAID]||style="background: #efefef;"|Collaborative Annotation Toolkit for Massive Amounts of Image Data. Enables collaborative tracing of neurons in serial section electron microscopy data and visualisation, sharing and collaborative annotation of imaging-based screens. Very ''Drosophila'' centric.||style="background: #efefef;"|Cardona Lab<br/> Janelia Research Campus<br/> Ashburn, VA, USA<br/>Tomancak lab<br/> Max Planck Institute of Molecular Cell Biology and Genetics<br/>Dresden, Germany
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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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| [http://www.openmicroscopy.org/site/products/omero OMERO] || OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Very general, well supported tool.||Swedlow Lab<br/> University of Dundee<br/> Dundee, UK
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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://www.cytomine.be/ Cytomine] ||style="background: #efefef;"| An open-source rich internet application for collaborative analysis of multi-gigapixel images. Focusing on histology data. ||style="background: #efefef;"|Systems and Modeling group<br/>University of Liège<br/>Liège, Belgium
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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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= Additional Useful CRISPR Links =
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!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;"| Reagents, protocols, and results from fly CRISPR/Cas9 experiments. ||style="background: #efefef;"| MRC Laboratory of Molecular Biology<br /> Cambridge, UK
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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="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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| [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;"| [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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|[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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*  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.
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* 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.
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*  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.
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*  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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*  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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*  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
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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
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= Selected recent CRISPR method reports for <em>in vivo</em> =
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* 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
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* 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
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* 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
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* 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
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* 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
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* 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
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* 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
 
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Revision as of 19:28, 8 August 2015

Popular Resource Categories

All Resources CRISPR RNAi Stocks Antibodies Images

This image-based resources page has been generously contributed by Pavel Tomancak of the Max Planck Institute of Molecular Cell Biology and Genetics.

Imaged Based Resources

Resource Description Author/Source
Patterns of gene expression in Drosophila embryogenesis Database of 2D images and annotations of patterns of gene expression during Drosophila embryogenesis revealed by RNA in situ hybridisation. Berkeley Drosophila Genome Project (BDGP)
Lawrence Berkeley National Laboratory
Berkeley, CA, USA
A database of Drosophila embryo and larvae mRNA localization patterns Database of 2D images and annotations of patterns of gene expression and RNA localisation in Drosophila embryos and larval tissues revealed by fluorescent RNA in situ hybridisation. Krause Lab
University of Toronto
Toronto, Ontario, Canada
Dresden Ovary Table Database of 3D images and annotations of patterns of RNA localisation in Drosophila ovaries revealed by fluorescent RNA in situ hybridisation. Tomancak lab
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
Expression Patterns of GAL4 and LexA Driver Lines Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in wing imaginal discs, larval nervous system and adult brain. Rubin, Truman, Doe, and Mann Labs
Janelia Research Campus
Ashburn, VA, USA
Fly Enhancers Database of 2D images and annotation of patterns driven by systematically generated enhancer constructs (Dickson collection) in embryos. Stark Lab
Research Institute of Molecular Pathology
Vienna, Austria
CRMs at BDGP Database of images and annotation of patterns driven by systematically generated enhancer constructs (Rubin collection) in embryos. Berkeley Drosophila Genome Project (BDGP)
Lawrence Berkeley National Laboratory
Berkeley, CA, USA
FLYtRAB Expression of 27 (all) endogenously tagged rab proteins in salivary glands, larval brain, wing discs, ovaries, testis and fat body imaged by high resolution confocal microscopy. Visualised in CATMAID. Eaton and Tomancak Labs
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
The FLAnnotator Database of images and annotations of Cambridge protein trap lines. St Johnston Lab
Wellcome Trust/Cancer Research UK Gurdon Institute
Cambridge, UK
MiMIC RMCE lines Database of images of MiMIC lines in larval CNS (GFP staining). Bellen Lab
Baylor College of Medicine
Houston, TX, USA
Virtual Fly Brain Sophisticated hub of Drosophila neuroanatomy data including several large sets of 3D scans of neuronal enhancer traps mapped onto a 3D atlas. Armstrong Lab
University of Edinburgh
Edinburgh, UK
Flytrap brain Vintage database of classical P(GAL4) enhancer traps imaged in head sections. Armstrong Lab
University of Edinburgh
Edinburgh, UK
Flytrap ovary - retired Deprecated database of Flytraps imaged in ovaries. Cooley Lab
Yale School of Medicine
New Haven, CT, USA


Tools for General Image Analysis

Resource Description Author/Source
ImageJ/Fiji Widely used open source platform for research in biological image analysis. Many plugins were developed around Drosophila centric projects. Eliceiri Lab
University of Wisconsin-Madison
Madison, WI, USA
Tomancak lab
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany
Vaa3D A platform aspiring to be a "Swiss army knife for big image data". Originally developed at Janelia Research Campus around Drosophila neurobiology projects. Peng Lab
Allen Institute
Washington, USA
Ilastik Simple, user-friendly tool for interactive image classification, segmentation and analysis. Brings the power of machine learning to biologists working with light and electron microscopy data. Build around Drosophila centric projects. NIG-FLY
National Institute of Genetics
Olivo-Marin Lab
Institut Pasteur
Paris, France
Icy Generalist open source image analysis platform with diverse functions. Not specifically connected to Drosophila research. Quantitative Image Analysis Unit
Institut Pasteur
Paris, France


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
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
FlyRNAi Blog, CRISPR tags A research blog tracking functional genomics techniques in Drosophila, filtered for keyword: CRISPRs. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
DRSC Single Cell Cloning Protocol Single-cell cloning method useful for Drosophila cell CRISPR gene editing. 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 recent CRISPR method reviews

Selected recent CRISPR method reports for tissue culture cells

Selected recent CRISPR method reports for in vivo


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