Resource Portal

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

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.	Drosophila RNAi Screening Center (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	Drosophila RNAi Screening Center (DRSC) Harvard Medical School Boston, MA, USA
Cell-Based RNAi Screen Summary	A summary of public cell-based DRSC screens	Drosophila RNAi Screening Center (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.

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All Resources

An extensive list of resources and reagents can be found on the pages linked below:

Drosophila Network Resources

Includes:

• Atlases, Images, and Videos
• CRISPRs and TALENs
• Data Repositories
• Data and Metadata for Drosophila Genomes
• Gene Expression Databases and Tools
• Gene Groups
• General Bioinformatics Tools
• Genome Sequencing Projects
• Human Disease: Drosophila Models and Orthologous Genes
• Interaction and Pathway Databases
• Laboratory Resources
• miRNA and ncRNA Databases and Tools
• Miscellaneous
• Ontology Resources
• Orthologs
• Phylogenetic Comparison Tools
• Population Biology and Polymorphism Resources
• Protein Analysis
• Public Education
• RNAi
• Sequence Analysis
• Taxonomy
• Transcription Regulation Databases and Tools

Drosophila Material Resources (Reagents)

Includes:

• Genomic Clones
• cDNA (EST Clones and Libraries)
• Arrays and Primers
• Stocks
• CRISPR Vectors
• Expression Vectors
• Cell Lines and Hybridomas
• Antibodies
• Transgenic, Targeted Mutation, and Other Services
• RNA
• RNAi

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