Difference between revisions of "Resource Portal"
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source | !style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source | ||
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− | |style="background: #efefef; white-space: nowrap;"| [https://kyotofly.kit.ac.jp/cgi-bin/ehime/index.cgi EHIME-Fly]||style="background: #efefef;"| Wild type stocks of Drosophila species that have been recorded in Japan. EHIME-Fly maintains and distributes over 130 species, represented by approximately 1450 stocks. ||style="background: #efefef; white-space: nowrap;"| Ehime University | + | |style="background: #efefef; white-space: nowrap;"| [https://kyotofly.kit.ac.jp/cgi-bin/ehime/index.cgi EHIME-Fly]||style="background: #efefef;"| Wild type stocks of Drosophila species that have been recorded in Japan. EHIME-Fly maintains and distributes over 130 species, represented by approximately 1450 stocks. ||style="background: #efefef; white-space: nowrap;"| Ehime University<br/> Matsuyama, Ehime Prefecture, Japan |
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− | | [https://stockcenter.ucsd.edu/info/welcome.php DSSC, Drosophila Species Stock Center] || The DSSC maintains a living collection of over 250 Drosophila species represented by approximately 1600 stocks || University of California | + | | [https://stockcenter.ucsd.edu/info/welcome.php DSSC, Drosophila Species Stock Center] || The DSSC maintains a living collection of over 250 Drosophila species represented by approximately 1600 stocks || University of California San Diego<br/> San Diego, CA, USA |
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− | |style="background: #efefef; white-space: nowrap;"| [http://www.shigen.nig.ac.jp/fly/kyorin/cgi-bin/index.cgi KYORIN-Fly ] ||style="background: #efefef;"| Mutant and wild type stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. ||style="background: #efefef;"| Kyorin University | + | |style="background: #efefef; white-space: nowrap;"| [http://www.shigen.nig.ac.jp/fly/kyorin/cgi-bin/index.cgi KYORIN-Fly ] ||style="background: #efefef;"| Mutant and wild type stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. ||style="background: #efefef;"| Kyorin University<br/> Shinkawa, Mitaka, Tokyo, Japan |
|} | |} | ||
Revision as of 18:49, 9 December 2015
FlyBase maintains extensive lists of useful external Network and Material Resources for fly researchers that can be accessed from the following links:
Network Resources
Reagent Resources
Links relevant to some of our most popular resources have been compiled and are listed below.
Popular Resources
CRISPR | RNAi | Stock Centers | Antibodies | Orthologs | All Resources |
Full Table of Contents
CRISPR
gRNA Design Resources
Resource | Description | Author/Source |
---|---|---|
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 numerous 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 numerous 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 5) using gene IDs, symbols, or chromosome locations. Allows for filtering of off-target sites and control of mis-match stringency. | Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA |
E-CRISPR | gRNA genome-wide (release 5) target finder, searchable via gene symbol or sequence. Support for numerous species (fly, zebrafish, mouse, human, others). Offers "relaxed, medium and strict" search options. | Boutros lab, DKFZ Heidelberg, Germany |
CHOPCHOP | Search for gRNA targets (release 5). Flexible inputs (gene name, genomic coordinates or DNA sequence) and detection of off-target sites. | Schier & Church Labs Harvard University Cambridge, MA, USA |
CRISPR Design | Identification of gRNA sites genome wide (release 5). Offers options for multiple species. | Zhang Lab MIT Boston, MA, USA |
CRISPOR | A program that helps design, evaluate, and clone guide sequences for the CRISPR/Cas9 system. Allows for searches across multiple species of Drosophila, including melanogaster (release 5). | Tefor France |
CRISPR Stocks
Resource | Description | Author/Source |
---|---|---|
CRISPR system stocks for site-specific mutagenesis | The Bloomington Stock Center's CRISPR/Cas9 page. Includes various stocks for expression of both Cas9 and tracrRNA. | Bloomington Drosophila Stock Center (BDSC) Indiana University Bloomington, IN, USA |
CRISPR Fly Design | Information on stocks generated by the CRISPR Fly Design group at the MRC Laboratory of Molecular Biology. | MRC Laboratory of Molecular Biology Cambridge, UK |
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 |
Additional Useful Links
Resource | Description | Author/Source |
---|---|---|
CRISPR Fly Design | An overview and resource collection for CRISPR gene editing in Drosophila. | 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 |
Selected recent methods 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.
- 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 methods 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 methods 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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RNAi
RNAi Design/Analysis Tools
Resource | Description | Author/Source |
---|---|---|
E-RNAi | E-RNAi is a tool for the design and evaluation of RNAi reagents. It can be used to design and evaluate long dsRNAs (including esiRNAs) as well as siRNAs. | Boutros lab, DKFZ Heidelberg, Germany |
NEXT-RNAi | Software for the design and evaluation of genome-wide RNAi libraries which performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context. | Boutros lab, DFKZ Heidelberg, Germany |
SnapDragon | A tool for the design of long dsRNAs for specific cell-based gene knockdown in Drosophila melanogaster via an RNAi approach. | Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA |
RNAi Stocks for in vivo studies (fly stocks)
Resource | Description | Author/Source |
---|---|---|
UP-TORR, Updated Targets of RNAi Reagents | A lookup tool for searching BDSC, TRiP, VDRC and NIG_FLY in vivo RNAi collections. | Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA |
BDSC RNAi Home Page | Links to lists and sublists of RNAi and miRNA sponge insertions at Bloomington. Most, but not all, of the insertions are under the control of UAS and therefore require GAL4 for expression. | Bloomington Drosophila Stock Center (BDSC) Indiana University Bloomington, IN, USA |
NIG_FLY | NIG-Fly in Mishima, Japan is part of a consortium with Kyoto-Fly and two other stock centers, and distributes RNAi flies on request. | NIG-FLY Mishima, Japan |
TRiP Transgenic RNAi Project | The TRiP Stock Collection contains over 9,000 lines, 1,575 of which are for orthologs of human-disease-associated genes. The stocks can be obtained from the BDSC. | Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA |
THFC, Tsinghua Fly Center | THFC RNAi Stock Collection for triggering RNAi in soma and germline | Tsinghua Fly Center Beijing, China |
VDRC, Vienna Drosophila Resource Center | The VDRC at IMP/IMBA in Vienna provides two genome-wide transgenic Drosophila RNAi libraries | VDRC Vienna, Austria |
Cell-based RNAi Reagents
Resource | Description | Author/Source |
---|---|---|
DRSC Libraries | Genome-Wide Libraries for cell-based RNAi Screening and Validation (on-site or shipped) | Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA |
Division of Signaling and Functional Genomics | Genome-Wide Libraries for cell-based RNAi Screening and Validation | Boutros lab, DKFZ, Heidelberg, Germany |
RNAi Screening Centers
Resource | Description | Author/Source |
---|---|---|
DRSC, Drosophila RNAi Screening Center | The Drosophila RNAi Screening Center at Harvard Medical School provides high throughput RNAi screens. | DRSC, Harvard Medical School, Boston, MA, USA |
NYU RNAi Screening and Automation Core | The NYU RNAi Core Facility at the Langone Medical Center in New York provides high-throughput RNAi screens. Drosophila screens are offered in collaboration with the DRSC. | NYU RNAi Core, New York, NY, USA |
Sheffield RNAi Screening Facility | The SRSF provides a service for whole-genome RNAi screens in Drosophila cells. | SRSF, University of Sheffield, Boston, MA, USA |
RNAi Results, Validation and Phenotypes
Resource | Description | Author/Source |
---|---|---|
GenomeRNAi | GenomeRNAi is a database containing phenotypes from cell-based and in vivo RNA interference (RNAi) screens in Drosophila. | GenomeRNAi, DKFZ, Heidelberg, Germany |
RSVP | RNAi Stock Validation and Phenotypes for in vivo RNAi studies | DRSC, Harvard Medical School, Boston, MA, USA |
Cell-Based RNAi Screen Summary | A summary of public cell-based DRSC screens | DRSC, Harvard Medical School, Boston, MA, USA |
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Stock Centers
List of D. melanogaster Stock Collections
Resource | Description | Author/Source |
---|---|---|
BDSC, Bloomington Drosophila Stock Center | A diverse collection of stocks useful for a wide range of research applications. | BDSC, Indiana University, Bloomington, IN, USA |
DGGR, Kyoto Stock Center | The Department of Drosophila Genomics and Genetics Resources collects, maintains and distributes Drosophila melanogaster strains for research. | DGGR, Kyoto, Japan |
Exelixis | The Exelixis Collection at Harvard Medical School | Harvard Medical School, Boston, MA, USA |
FlyORF | Well characterized transgenic UAS-ORF lines. Approximately 2,400 fly stocks comprising about 1900 genes, generated using the phiC31 integrase method | FlyORF, University of Zurich, Zurich, Switzerland |
NIG-FLY | NIG-RNAi stocks and TRiP Stocks for RNA interference experiments | NIG-FLY, National Institute of Genetics, Mishima, Japan |
CRISPR system stocks for site-specific mutagenesis | CRISPR system stocks for site-specific mutagenesis at BDSC | BDSC, Indiana University, Bloomington, IN, USA |
Tsinghua Fly Center (THFC) | Transgenic RNAi fly lines | THFC, Tsinghua University, Beijing, China |
VDRC, Vienna Drosophila RNAi Center | Trangenic Drosophila RNAi libraries, a collection of enhancer-GAL4 driver lines, the Tagged FlyFos TransgeneOme (fTRG) library | VDRC, Vienna, Austria |
D. melanogaster Stock Collection Informational Sites
Resource | Description | Author/Source |
---|---|---|
CRISPR fly design | Details of a set of cas9 transgenic D. melanogaster lines which are available at the BDSC | MRC-Laboratory of Molecular Biology, Cambridge, UK |
DrosDel An isogenic deficiency kit for Drosophila melanogaster | Information about isogenic deficiency lines generated by the DrosDel Project | University of Cambridge, Cambridge, UK |
Flytrap Project | Information about GFP protein trap lines from the FlyTrap project | Yale University, New Haven, CT, USA |
Gene Disruption Project | Information about insertion lines produced by the Gene Disruption Project (GDP) | Baylor College of Medicine, Houston, TX, USA |
Gene Disruption Project | Information about MiMIC RMCE Lines | Baylor College of Medicine, Houston, TX, USA |
Ehime University fly species photographs | Photograph of 102 species of Drosophila in Drosophila stocks of Ehime University. | Ehime University, Matsuyama, Ehime, Japan |
List of Drosophila Species Collections
Resource | Description | Author/Source |
---|---|---|
EHIME-Fly | Wild type stocks of Drosophila species that have been recorded in Japan. EHIME-Fly maintains and distributes over 130 species, represented by approximately 1450 stocks. | Ehime University Matsuyama, Ehime Prefecture, Japan |
DSSC, Drosophila Species Stock Center | The DSSC maintains a living collection of over 250 Drosophila species represented by approximately 1600 stocks | University of California San Diego San Diego, CA, USA |
KYORIN-Fly | Mutant and wild type stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. | Kyorin University Shinkawa, Mitaka, Tokyo, Japan |
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Antibodies
Links to collections of Drosophila-specific antibodies.
Resource | Author/Source |
---|---|
Abbiotec | San Diego, CA, USA |
Abcam | Cambridge, MA, USA |
Acris Antibodies | San Diego, CA, USA Herford, Germany |
Active Motif | Carlsbad, CA, USA International Locations |
Biorbyt | Cambridge, UK |
Cell Signaling Technology | Danvers, MA, USA International Locations |
Developmental Studies Hybridoma Bank (DSHB) | University of Iowa Iowa City, IA, USA |
FabGennix | Frisco, TX, USA |
GeneTex | Irvine, CA, USA International Locations |
Novus | Littleton, CO, USA |
ProSci | Poway, CA, USA |
R&D Systems | Minneapolis, MN, USA |
Santa Cruz Biotechnology | Dallas, Texas, USA |
Sigma Aldrich (additional link) | St. Louis, MO, USA International Locations |
Links to vendors whose collections include Drosophila-specific antibodies.
The table below contains non-direct Drosophila antibody links, additional searching is required from the vendor website.
Resource | Author/Source |
---|---|
Abgent | San Diego, CA, USA Suzhou city, Jiangsu Province, China |
antibodies-online | International Locations |
Enzo Life Sciences | Farmingdale, NY, USA |
LifeSpan BioSciences | Seattle, WA, USA |
Thermo Fisher | Waltham, MA, USA |
Lab-generated antibodies in Gene Reports
Antibodies generated by research laboratories for specific proteins are listed in their respective Gene Report under "Stocks and Reagents" → "Antibody Information".
For example, the following screenshot is taken from the Notch gene report:
If no antibodies exist or they have not yet been curated, this section will be empty.