FlyBase:Images
Revision as of 19:28, 8 August 2015 by ChrisTabone (talk | contribs)
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
- 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 recent 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.
- 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
- 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
- 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
Selected recent CRISPR method reports for in vivo
- 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
- 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
- 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
- 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
- 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
- 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, 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
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