Difference between revisions of "Resource Portal"

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<span style="color: red;">'''**This page is a work-in-progress concept of reformatting our resource and reagent list.**'''</span>
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FlyBase maintains extensive lists of useful external Network and Material Resources for fly researchers that can be accessed from the following links:<br />
 +
'''[http://flybase.org/wiki/FlyBase:Drosophila_Network_Resources Network Resources]'''<br/>
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'''[http://flybase.org/wiki/FlyBase:Drosophila_Material_Resources Reagent Resources]'''<br/>
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Links relevant to some of our most  popular resources have been compiled and are listed below.
  
 
= Popular Resources =
 
= Popular Resources =
  
{|class="wikitable" style="margin: 1em auto 1em auto;"
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{|class="wikitable"  
 
|-
 
|-
|style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#Stock_Centers|Stock Centers]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Antibodies]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Other Example]]</big>
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|style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#Stock_Centers|Stock Centers]]</big> ||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#Antibodies|Antibodies]]</big>||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#Orthologs|Orthologs]]</big>||style="text-align: center; padding: 20px;"| <big>[[Resource_Portal#All_Resources|All Resources]]</big>
 
|}
 
|}
  
== CRISPR ==
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== Full Table of Contents ==
  
=== Introduction ===
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__TOC__
  
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aliquam vel vehicula risus. Ut id magna odio. Proin in bibendum odio, non dictum justo. Cras vitae eros arcu. Vestibulum porttitor nibh sit amet justo venenatis, vel tempor erat fringilla. Sed elementum varius ante. Donec eget neque mi. Vestibulum id nisi sit amet purus auctor porta eu quis elit. Nulla facilisi. Sed semper scelerisque ex, eu aliquet libero sollicitudin a.
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== CRISPR ==
  
 
=== gRNA Design Resources ===
 
=== gRNA Design Resources ===
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{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
|-
 
|-
|style="background: #efefef;"| [http://www.flyrnai.org/crispr2/ DRSC Find CRISPR Tool] ||style="background: #efefef;"| DRSC<br /> Harvard Medical School<br /> Boston, USA ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Duis posuere nisl eget nunc congue fermentum. Duis hendrerit auctor nulla convallis molestie. Donec maximus congue odio quis efficitur. Etiam commodo nulla ut tincidunt vehicula. Integer pulvinar dui id vulputate pulvinar. Suspendisse potenti.
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|style="white-space: nowrap; background: #efefef;"| [http://tools.flycrispr.molbio.wisc.edu/targetFinder/ CRISPR Optimal Target Finder] ||style="background: #efefef;"| Identifies gRNA targets within a provided sequence and additionally searches genome-wide ('''release 6, current FlyBase release''') for potential off-target sites. Includes numerous <em>Drosophila</em> species.||style="white-space: nowrap; background: #efefef;"|O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA
 
|-
 
|-
|style="white-space: nowrap;"| [http://tools.flycrispr.molbio.wisc.edu/targetFinder/ CRISPR Optimal Target Finder] ||style="white-space: nowrap;"| O'Connor-Giles, Wildonger, and Harrison Labs<br /> University of Wisconsin-Madison<br /> WI, USA|| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam eu nibh scelerisque, egestas ante ac, commodo dui. Vestibulum finibus ultricies urna eu hendrerit. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Phasellus at nisl tincidunt, placerat mauris a, sodales ex. Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos.
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| [http://www.crisprscan.org/ 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<br /> Yale University<br /> New Haven, CT, USA
 
|-
 
|-
|style="background: #efefef;"| [http://www.e-crisp.org/E-CRISP/designcrispr.html E-CRISPR] ||style="background: #efefef;"| DKFZ/Boutros Lab<br /> Heildelberg, Germany ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Etiam et congue elit. Aliquam sapien mi, semper eu varius ac, fermentum quis purus. Praesent mollis porttitor pretium.
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|style="background: #efefef;"|[http://www.flyrnai.org/crispr2/ DRSC Find CRISPR Tool] ||style="background: #efefef;"| 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. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|-
 
|-
| [https://chopchop.rc.fas.harvard.edu/ CHOPCHOP] || Schier & Church Labs<br /> Harvard University<br /> Cambridge, USA || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras auctor nisi accumsan pulvinar consequat. Vestibulum ante ipsum primis in faucibus orci luctus et ultrices posuere cubilia Curae; Etiam elit nunc, facilisis eget faucibus eu, porta pulvinar justo.
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| [http://www.e-crisp.org/E-CRISP/designcrispr.html 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<br/> Heidelberg, Germany
 
|-
 
|-
|style="background: #efefef;"| [http://crispr.mit.edu/ Genome Engineering] ||style="background: #efefef;"| Zhang Lab<br /> MIT<br /> Boston, MA, USA ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
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|style="background: #efefef;"| [https://chopchop.rc.fas.harvard.edu/ CHOPCHOP] ||style="background: #efefef;"| Search for gRNA targets (release 5). Flexible inputs (gene name, genomic coordinates or DNA sequence) and detection of off-target sites.  ||style="background: #efefef;"| Schier & Church Labs<br /> Harvard University<br /> Cambridge, MA, USA
 
|-
 
|-
| [http://www.crisprscan.org/ CRISPRscan] || Giraldez Lab<br /> Yale University<br /> New Haven, USA || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aliquam ut nibh diam. Duis sed sapien odio. Donec lectus nisl, congue non erat ac, aliquet faucibus ligula. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas.
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| [http://crispr.mit.edu/ CRISPR Design] ||Identification of gRNA sites genome wide (release 5). Offers options for multiple species. || Zhang Lab<br /> MIT<br /> Boston, MA, USA  
 
|-
 
|-
|style="background: #efefef;"| [http://tefor.net/crispor/crispor.cgi CRISPOR] ||style="background: #efefef;"| Tefor<br />France ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam et tincidunt ante. Donec tincidunt gravida velit at iaculis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean rutrum quam eget luctus condimentum. Cras in venenatis lectus, at laoreet augue.
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|style="background: #efefef;"| [http://tefor.net/crispor/crispor.cgi CRISPOR] ||style="background: #efefef;"| A program that helps design, evaluate, and clone guide sequences for the CRISPR/Cas9 system. Allows for searches across multiple species of <em>Drosophila</em>, including melanogaster (release 5).||style="background: #efefef;"| Tefor<br />France
 
|-
 
|-
| [http://crispr-era.stanford.edu/ CRISPR-ERA] || Lei Stanley Qi Lab and Xiaowo Wang Lab<br /> Stanford University<br /> Standford, USA || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec aliquam erat id nisl posuere, nec euismod metus sodales. Etiam ligula libero, auctor eu feugiat a, cursus eget risus. Cras placerat dui magna, non tincidunt neque auctor vitae. Nullam ullamcorper tortor id augue scelerisque convallis.
 
 
|}
 
|}
 +
<br/>
 +
 
=== CRISPR Stocks ===
 
=== CRISPR Stocks ===
  
 
{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
|-
 
|style="background: #efefef; white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef; white-space: nowrap;"| Bloomington Stock Center ||style="background: #efefef;"| Stocks used to express Cas9 nuclease and/or tracrRNA maternally so that chimeric RNAs (also referred to as guide RNAs) or CRISPR RNAs (crRNAs) can be injected into fly embryos to generate new mutations without the need for helper plasmids, or so that they can be used in combination with chimeric or CRISPR RNAs expressed from transgenic constructs.
 
 
|-
 
|-
| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || MRC - Laboratory of Molecular Biology || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
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|style="white-space: nowrap; background: #efefef;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef;"| The Bloomington Stock Center's CRISPR/Cas9 page. Includes various stocks for expression of both Cas9 and tracrRNA. ||style="background: #efefef;"| Bloomington Drosophila Stock Center (BDSC)<br/> Indiana University<br/> Bloomington, IN, USA
 
|-
 
|-
|style="background: #efefef;"| [http://www.flyrnai.org/TRiP-TBX.html The TRiP Toolbox Stocks] ||style="background: #efefef;"| Example ||style="background: #efefef;"| Example
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| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || Information on stocks generated by the CRISPR Fly Design group at the MRC Laboratory of Molecular Biology.  ||style="white-space: nowrap;"| MRC Laboratory of Molecular Biology<br />
 +
Cambridge, UK
 
|-
 
|-
| Example || Example || Example
 
 
|}
 
|}
 +
<br/>
  
 
=== CRISPR Vectors ===
 
=== CRISPR Vectors ===
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{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
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!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|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
 +
|-
 +
| [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
 +
|}
 +
<br/>
 +
=== Additional Useful Links ===
 +
{|cellpadding=5
 
|-
 
|-
|style="background: #efefef; white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef; white-space: nowrap;"| Bloomington Stock Center ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam et tincidunt ante. Donec tincidunt gravida velit at iaculis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean rutrum quam eget luctus condimentum. Cras in venenatis lectus, at laoreet augue.
+
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
|-
 
|-
| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || MRC - Laboratory of Molecular Biology || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
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|style="white-space: nowrap; background: #efefef;"| [http://www.crisprflydesign.org/ CRISPR Fly Design]||style="white-space: nowrap; background: #efefef;"| An overview and resource collection for CRISPR gene editing in <em>Drosophila</em>. ||style="background: #efefef;"| MRC Laboratory of Molecular Biology<br />
 +
Cambridge, UK
 
|-
 
|-
|style="background: #efefef;"| Example ||style="background: #efefef;"| Example ||style="background: #efefef;"| Example
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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
 
|-
 
|-
| Example || Example || Example
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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
 +
|-
 +
| [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
 +
|-
 +
|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
 
|}
 
|}
=== CRISPR Methods Publications ===
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<br/>
 +
 
 +
=== Selected recent methods reviews ===
  
* [http://www.ncbi.nlm.nih.gov/pubmed/26447401 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<nowiki>]</nowiki> Review. PubMed PMID: 26447401.]
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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.
 +
*  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.
 +
*  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.
  
 +
=== Selected recent methods reports for tissue culture cells ===
 +
 +
*  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.
 +
*  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
 +
*  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
 +
* 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
 +
 +
=== Selected recent methods reports for <em>in vivo</em> ===
 +
* 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
 +
 +
* 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
 +
 +
* 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
 +
 +
* 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
 +
 +
* 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
 +
 +
* 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
 +
 +
* 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
 
<br>
 
<br>
 
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
 
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
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== RNAi ==
 
== RNAi ==
  
=== Introduction ===
 
  
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aliquam vel vehicula risus. Ut id magna odio. Proin in bibendum odio, non dictum justo. Cras vitae eros arcu. Vestibulum porttitor nibh sit amet justo venenatis, vel tempor erat fringilla. Sed elementum varius ante. Donec eget neque mi. Vestibulum id nisi sit amet purus auctor porta eu quis elit. Nulla facilisi. Sed semper scelerisque ex, eu aliquet libero sollicitudin a.
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=== RNAi Design/Analysis Tools ===
 +
 
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef; white-space"| [http://www.dkfz.de/signaling/e-rnai3/ E-RNAi]||style="background: #efefef; white-space:"| 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. ||style="background: #efefef;"| Boutros lab, DKFZ<br/> Heidelberg, Germany
 +
|-
 +
| [http://b110-wiki.dkfz.de/confluence/display/nextrnai/NEXT-RNAi 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<br/> Heidelberg, Germany
 +
|-
 +
|style="background: #efefef;"| [http://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl SnapDragon] ||style="background: #efefef;"| A tool for the design of long dsRNAs for specific cell-based gene knockdown in Drosophila melanogaster via an RNAi approach. ||style="background: #efefef; white-space: nowrap"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 +
|}
 +
<br/>
  
=== RNAi Design Resources ===
+
=== RNAi Stocks for in vivo studies (fly stocks) ===
  
 
{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
+
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
|-
 
|-
|style="background: #efefef; white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef; white-space: nowrap;"| Bloomington Stock Center ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam et tincidunt ante. Donec tincidunt gravida velit at iaculis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean rutrum quam eget luctus condimentum. Cras in venenatis lectus, at laoreet augue.
+
| [http://www.flyrnai.org/up-torr/ 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)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|-
 
|-
| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || MRC - Laboratory of Molecular Biology || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
+
|style="background: #efefef; white-space:"| [http://flystocks.bio.indiana.edu/Browse/RNAi/RNAihome.htm BDSC RNAi Home Page]||style="background: #efefef; white-space:"| 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. ||style="background: #efefef; white-space:nowrap"| Bloomington Drosophila Stock Center (BDSC)<br/> Indiana University<br/> Bloomington, IN, USA
 
|-
 
|-
|style="background: #efefef;"| Example ||style="background: #efefef;"| Example ||style="background: #efefef;"| Example
+
| [http://www.shigen.nig.ac.jp/fly/nigfly/index.jsp 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<br/> Mishima, Japan
 
|-
 
|-
| Example || Example || Example
+
|style="background: #efefef;"| [http://www.flyrnai.org/TRiP-HOME.html TRiP Transgenic RNAi Project] ||style="background: #efefef;"| 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. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 +
|-
 +
| [http://center.biomed.tsinghua.edu.cn/public/eq-category/modelanimalfacility/ THFC, Tsinghua Fly Center] || THFC RNAi Stock Collection for triggering RNAi in soma and germline || Tsinghua Fly Center<br/> Beijing, China
 +
|-
 +
|style="background: #efefef;"| [http://stockcenter.vdrc.at/control/main VDRC, Vienna Drosophila Resource Center] ||style="background: #efefef;"| The VDRC at IMP/IMBA in Vienna provides two genome-wide transgenic Drosophila RNAi libraries ||style="background: #efefef;"| VDRC<br/> Vienna, Austria
 
|}
 
|}
=== RNAi Stocks ===
+
<br/>
 +
 
 +
=== Cell-based RNAi Reagents ===
  
 
{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
+
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 
|-
 
|-
|style="background: #efefef; white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef; white-space: nowrap;"| Bloomington Stock Center ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam et tincidunt ante. Donec tincidunt gravida velit at iaculis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean rutrum quam eget luctus condimentum. Cras in venenatis lectus, at laoreet augue.
+
|style="background: #efefef; white-space:"| [http://www.flyrnai.org/DRSC-DRS.html DRSC Libraries]||style="background: #efefef; white-space:"| Genome-Wide Libraries for cell-based RNAi Screening and Validation (on-site or shipped) ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|-
 
|-
| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || MRC - Laboratory of Molecular Biology || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
+
| [http://www.dkfz.de/signaling/ Division of Signaling and Functional Genomics] || Genome-Wide Libraries for cell-based RNAi Screening and Validation || Boutros lab, DKFZ, Heidelberg, Germany
 +
|}
 +
<br/>
 +
 
 +
=== RNAi Screening Centers ===
 +
 
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef; white-space"| [http://www.flyrnai.org/RNAi_index.html DRSC, Drosophila RNAi Screening Center]||style="background: #efefef; white-space:"| The Drosophila RNAi Screening Center at Harvard Medical School provides high throughput RNAi screens. ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 +
|-
 +
|style="nowrap;"| [http://www.med.nyu.edu/ocs/rnai/ 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
 +
|-
 +
|style="background: #efefef;"| [http://www.rnai.group.shef.ac.uk/ Sheffield RNAi Screening Facility] ||style="background: #efefef;"| The SRSF provides a service for whole-genome RNAi screens in Drosophila cells. ||style="background: #efefef;"| SRSF, University of Sheffield, Boston, MA, USA
 +
|}
 +
<br/>
 +
 
 +
=== RNAi Results, Validation and Phenotypes ===
 +
 
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef; white-space"| [http://www.genomernai.org/ GenomeRNAi] ||style="background: #efefef; white-space:"| GenomeRNAi is a database containing phenotypes from cell-based and in vivo RNA interference (RNAi) screens in Drosophila. ||style="background: #efefef;"| GenomeRNAi, DKFZ, Heidelberg, Germany
 
|-
 
|-
|style="background: #efefef;"| Example ||style="background: #efefef;"| Example ||style="background: #efefef;"| Example
+
|style="nowrap;"| [http://www.flyrnai.org/RSVP RSVP] || RNAi Stock Validation and Phenotypes for in vivo RNAi studies || Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|-
 
|-
| Example || Example || Example
+
|style="background: #efefef;"| [http://www.flyrnai.org/screensummary Cell-Based RNAi Screen Summary] ||style="background: #efefef;"| A summary of public cell-based DRSC screens ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|}
 
|}
  
Line 116: Line 199:
 
==Stock Centers==
 
==Stock Centers==
  
=== List of Drosophila Stock Centers ===
+
 
 +
=== List of D. melanogaster Stock Collections ===
  
 
{|cellpadding=5
 
{|cellpadding=5
 
|-
 
|-
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source !!style="background: #efefef;"| Additional Information
+
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef;"| [http://flystocks.bio.indiana.edu/ BDSC, Bloomington Drosophila Stock Center] ||style="background: #efefef;"| A diverse collection of stocks useful for a wide range of research applications. ||style="background: #efefef;"| BDSC, Indiana University, Bloomington, IN, USA
 +
|-
 +
| [https://kyotofly.kit.jp/cgi-bin/stocks/index.cgi DGGR, Kyoto Stock Center] || The Department of Drosophila Genomics and Genetics Resources collects, maintains and distributes Drosophila melanogaster strains for research. || DGGR, Kyoto, Japan
 
|-
 
|-
|style="background: #efefef; white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style="background: #efefef; white-space: nowrap;"| Bloomington Stock Center ||style="background: #efefef;"| Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nullam et tincidunt ante. Donec tincidunt gravida velit at iaculis. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean rutrum quam eget luctus condimentum. Cras in venenatis lectus, at laoreet augue.
+
|style="background: #efefef;"| [https://drosophila.med.harvard.edu/ Exelixis] ||style="background: #efefef;"| The Exelixis Collection at Harvard Medical School||style="background: #efefef;"| Harvard Medical School, Boston, MA, USA
 
|-
 
|-
| [http://www.crisprflydesign.org/flies/ CRISPR Fly Design] || MRC - Laboratory of Molecular Biology || Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer id purus metus. Cras et lacus vel diam posuere facilisis. Vestibulum lorem metus, dapibus nec porta non, fringilla sit amet eros.
+
| [http://flyorf.ch/ 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
 
|-
 
|-
|style="background: #efefef;"| Example ||style="background: #efefef;"| Example ||style="background: #efefef;"| Example
+
|style="background: #efefef;"| [http://www.shigen.nig.ac.jp/fly/nigfly/ NIG-FLY] ||style="background: #efefef;"| NIG-RNAi stocks and TRiP Stocks for RNA interference experiments ||style="background: #efefef;"| NIG-FLY, National Institute of Genetics, Mishima, Japan
 
|-
 
|-
| Example || Example || Example
+
|style="white-space: nowrap;"| [http://flystocks.bio.indiana.edu/Browse/misc-browse/CRISPR.htm CRISPR system stocks for site-specific mutagenesis]||style=" white-space: nowrap;"| CRISPR system stocks for site-specific mutagenesis at BDSC || BDSC, Indiana University, Bloomington, IN, USA
 +
|-
 +
|style="background: #efefef;"| [http://center.biomed.tsinghua.edu.cn/public/eq-category/modelanimalfacility/ Tsinghua Fly Center (THFC)] ||style="background: #efefef;"| Transgenic RNAi fly lines ||style="background: #efefef;"| THFC, Tsinghua University, Beijing, China
 +
|-
 +
| [http://stockcenter.vdrc.at/control/main 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
 
|}
 
|}
 +
<br/>
 +
 +
=== D. melanogaster Stock Collection Informational Sites ===
 +
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef;"| [http://www.crisprflydesign.org/flies/ CRISPR fly design] ||style="background: #efefef;"| Details of a set of cas9 transgenic D. melanogaster lines which are available at the BDSC ||style="background: #efefef;"| MRC-Laboratory of Molecular Biology, Cambridge, UK
 +
|-
 +
| [http://www.drosdel.org.uk/ DrosDel An isogenic deficiency kit for Drosophila melanogaster]|| Information about isogenic deficiency lines generated by the DrosDel Project || University of Cambridge, Cambridge, UK
 +
|-
 +
|style="background: #efefef;"| [http://cooley.medicine.yale.edu/flytrap/ Flytrap Project] ||style="background: #efefef;"| Information about GFP protein trap lines from the FlyTrap project ||style="background: #efefef;"| Yale University, New Haven, CT, USA
 +
|-
 +
| [http://flypush.imgen.bcm.tmc.edu/pscreen/ Gene Disruption Project] || Information about insertion lines produced by the Gene Disruption Project (GDP) || Baylor College of Medicine, Houston, TX, USA
 +
|-
 +
|style="background: #efefef;"| [http://flypush.imgen.bcm.tmc.edu/pscreen/rmce/ Gene Disruption Project] ||style="background: #efefef;"| Information about MiMIC RMCE Lines ||style="background: #efefef;"| Baylor College of Medicine, Houston, TX, USA
 +
|-
 +
| [http://www.ehime-u.ac.jp/~scibio/evolut/DSEU_photo/ Ehime University fly species photographs] || Photograph of 102 species of Drosophila in Drosophila stocks of Ehime University. || Ehime University, Matsuyama, Ehime, Japan
 +
|}
 +
<br/>
 +
 +
=== List of Drosophila Species Collections ===
 +
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Description !!style="background: #efefef;"| Author/Source
 +
|-
 +
|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
 +
|-
 +
| [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
 +
|-
 +
|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
 +
|}
 +
 +
 +
<br>
 +
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
 +
 +
== Antibodies ==
 +
 +
===Links to collections of <em>Drosophila</em>-specific antibodies.===
 +
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef;"| [http://www.abbiotec.com/antibodies?populate=&field_antibody_subcategory_tid=All&field_isotype_value=All&field_species_reactivity_value=Ds&field_applications_value=All&field_protein_family_tid=All Abbiotec] ||style="background: #efefef;"|San Diego, CA, USA
 +
|-
 +
|[http://www.abcam.com/products?keywords=drosophila&selected.classification=Primary+antibodies&selected.reactivity=Fruit+fly+(Drosophila+melanogaster) Abcam] ||Cambridge, MA, USA
 +
|-
 +
|style="background: #efefef;"|[https://us.acris-antibodies.com/antibodies/primary-antibodies.htm?ab_ag_reactivity=Dros Acris Antibodies] ||style="background: #efefef;"|San Diego, CA, USA<br/> Herford, Germany
 +
|-
 +
|[https://www.activemotif.com/catalog/806/search-browse-all-antibodies?svs_product_class=Antibodies&mvs_reactivity=Drosophila Active Motif] ||Carlsbad, CA, USA <br/>International Locations
 +
|-
 +
|style="background: #efefef;"| [http://www.biorbyt.com/products/antibodies?speciesselect=51 Biorbyt] ||style="background: #efefef;"| Cambridge, UK<br/>
 +
|-
 +
| [http://www.cellsignal.com/browse/d-melanogaster?N=4294956287+4294964832+4294960387 Cell Signaling Technology] || Danvers, MA, USA<br/> International Locations
 +
|-
 +
|style="background: #efefef;"| [http://dshb.biology.uiowa.edu/Antibody-Collections/Drosophila-antigens Developmental Studies Hybridoma Bank (DSHB)] ||style="background: #efefef;"| University of Iowa<br/>
 +
Iowa City, IA, USA
 +
|-
 +
| [http://fabgennix.com/epages/862cc93a-7f43-4d98-8516-1e11a7720fd8.sf/en_US/?ObjectID=81707&ViewAction=ViewFaceted&FacetValue_CategoryID=81707&FacetValue_PreDefString_en_1540487778=D.+melanogaster&CurrencyID=USD&CurrencyID=USD&FacetRange_ListPrice=&FacetRange_ListPrice= FabGennix] || Frisco, TX, USA
 +
|-
 +
|style="background: #efefef;"| [http://www.genetex.com/Web/search/Catalog.aspx?Type=1&Category=494&Reactivity=Drosophila&Page=1 GeneTex] ||style="background: #efefef;"| Irvine, CA, USA<br/>International Locations
 +
|-
 +
|| [http://www.novusbio.com/drosophilaantibodies.html Novus]|| Littleton, CO, USA
 +
|-
 +
|style="background: #efefef;"| [http://www.prosci-inc.com/primary-antibodies.html?species_reactivity=601 ProSci] ||style="background: #efefef;"| Poway, CA, USA
 +
|-
 +
|| [https://www.rndsystems.com/search?keywords=primary%20antibodies&species=Drosophila R&D Systems]|| Minneapolis, MN, USA
 +
|-
 +
|style="background: #efefef;"| [http://www.scbt.com/section/primary_antibodies_non-mammalian/drosophila_proteins.html Santa Cruz Biotechnology]||style="background: #efefef;"| Dallas, Texas, USA
 +
|-
 +
|| [http://www.sigmaaldrich.com/catalog/search?interface=All&N=0+14574647+4294666762&mode=partialmax&focus=product&lang=en&region=US Sigma Aldrich] ([http://www.sigmaaldrich.com/catalog/search?interface=All&N=0+14574647+4294666151&mode=partialmax&focus=product&lang=en&region=US additional link])|| St. Louis, MO, USA <br/> International Locations
 +
|}
 +
 +
<br>
 +
 +
===Links to vendors whose collections include <em>Drosophila</em>-specific antibodies.===
 +
 +
The table below contains non-direct <em>Drosophila</em> antibody links, additional searching is required from the vendor website.
 +
 +
{|cellpadding=5
 +
|-
 +
!style="background: #efefef;"| Resource !!style="background: #efefef;"| Author/Source
 +
|-
 +
|style="background: #efefef;"| [http://www.abgent.com/ Abgent] ||style="background: #efefef; whitespace:no-wrap;"|San Diego, CA, USA <br/> Suzhou city, Jiangsu Province, China
 +
|-
 +
|[http://www.antibodies-online.com/ antibodies-online] ||International Locations
 +
|-
 +
|style="background: #efefef;"|[http://www.enzolifesciences.com/ Enzo Life Sciences] ||style="background: #efefef;"|Farmingdale, NY, USA
 +
|-
 +
|[https://www.lsbio.com/ LifeSpan BioSciences] ||Seattle, WA, USA
 +
|-
 +
|style="background: #efefef;"|[https://www.thermofisher.com/us/en/home.html Thermo Fisher] || style="background: #efefef;"|Waltham, MA, USA
 +
|}
 +
 +
<br/>
 +
 +
===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'''" &#8594; "'''Antibody Information'''".
 +
<br/>
 +
For example, the following screenshot is taken from the [http://flybase.org/reports/FBgn0004647.html Notch gene report]:<br/> <br/>
 +
[[File:Antibodies.png|800px]]
 +
<br/><br/>
 +
If no antibodies exist or they have not yet been curated, this section will be empty.
  
 
<br>
 
<br>
 
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
 
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
  
= Additional Resources =
+
=All Resources=
 +
An extensive list of resources and reagents can be found on the pages linked below:
 +
 
 +
<big>'''[[FlyBase:Drosophila Network Resources|Drosophila Network Resources]]'''</big>
 +
 
 +
Includes:
 +
*[[FlyBase:Drosophila_Network_Resources#Atlases.2C_Images_and_Videos|Atlases, Images, and Videos]]
 +
* [[FlyBase:Drosophila_Network_Resources#CRISPRs_and_TALENs|CRISPRs and TALENs]]
 +
* [[FlyBase:Drosophila_Network_Resources#Data_Repositories|Data Repositories]]
 +
* [[FlyBase:Drosophila_Network_Resources#Data_and_Metadata_for_Drosophila_Genomes|Data and Metadata for Drosophila Genomes]]
 +
* [[FlyBase:Drosophila_Network_Resources#Gene_Expression_Databases_and_Tools|Gene Expression Databases and Tools]]
 +
*[[FlyBase:Drosophila_Network_Resources#Gene_Groups|Gene Groups]]
 +
* [[FlyBase:Drosophila_Network_Resources#General_Bioinformatics_Tools|General Bioinformatics Tools]]
 +
* [[FlyBase:Drosophila_Network_Resources#Genome_Sequencing_Projects|Genome Sequencing Projects]]
 +
* [[FlyBase:Drosophila_Network_Resources#Human_Disease:_Drosophila_Models_and_Orthologous_Genes|Human Disease: Drosophila Models and Orthologous Genes]]
 +
* [[FlyBase:Drosophila_Network_Resources#Interaction_and_Pathway_Databases|Interaction and Pathway Databases]]
 +
* [[FlyBase:Drosophila_Network_Resources#Laboratory_Resources|Laboratory Resources]]
 +
* [[FlyBase:Drosophila_Network_Resources#miRNA_and_ncRNA_Databases_and_Tools|miRNA and ncRNA Databases and Tools]]
 +
* [[FlyBase:Drosophila_Network_Resources#Miscellaneous|Miscellaneous]]
 +
* [[FlyBase:Drosophila_Network_Resources#Ontology_Resources|Ontology Resources]]
 +
* [[FlyBase:Drosophila_Network_Resources#Ontology_Resources|Orthologs]]
 +
* [[FlyBase:Drosophila_Network_Resources#Phylogenetic_Comparison_Tools|Phylogenetic Comparison Tools]]
 +
* [[FlyBase:Drosophila_Network_Resources#Population_Biology_and_Polymorphism_Resources|Population Biology and Polymorphism Resources]]
 +
* [[FlyBase:Drosophila_Network_Resources#Protein_Analysis|Protein Analysis]]
 +
* [[FlyBase:Drosophila_Network_Resources#Public_Education|Public Education]]
 +
* [[FlyBase:Drosophila_Network_Resources#RNAi|RNAi]]
 +
* [[FlyBase:Drosophila_Network_Resources#Sequence_Analysis|Sequence Analysis]]
 +
* [[FlyBase:Drosophila_Network_Resources#Taxonomy|Taxonomy]]
 +
* [[FlyBase:Drosophila_Network_Resources#Transcription_Regulation_Databases_and_Tools|Transcription Regulation Databases and Tools]]
  
* This section would contain links to additional resource pages or a copy+pasted version of the old resource page.
+
<big>'''[[FlyBase:Drosophila Material Resources|Drosophila Material Resources (Reagents)]]'''</big>
 +
 
 +
Includes:
 +
* [[FlyBase:Drosophila_Material_Resources#Genomic_Clones|Genomic Clones]]
 +
* [[FlyBase:Drosophila_Material_Resources#cDNA_.28EST_Clones_and_Libraries.29|cDNA (EST Clones and Libraries)]]
 +
* [[FlyBase:Drosophila_Material_Resources#Arrays_and_Primers|Arrays and Primers]]
 +
* [[FlyBase:Drosophila_Material_Resources#Stocks|Stocks]]
 +
* [[FlyBase:Drosophila_Material_Resources#Stocks|CRISPR Vectors]]
 +
* [[FlyBase:Drosophila_Material_Resources#Expression_Vectors|Expression Vectors]]
 +
* [[FlyBase:Drosophila_Material_Resources#Cell_Lines_and_Hybridomas|Cell Lines and Hybridomas]]
 +
* [[FlyBase:Drosophila_Material_Resources#Antibodies|Antibodies]]
 +
* [[FlyBase:Drosophila_Material_Resources#Transgenic.2C_Targeted_Mutation.2C_and_Other_Services|Transgenic, Targeted Mutation, and Other Services]]
 +
* [[FlyBase:Drosophila_Material_Resources#RNA|RNA]]
 +
* [[FlyBase:Drosophila_Material_Resources#RNAi|RNAi]]
 +
 
 +
<br>
 +
&nbsp; [[Resource_Portal#top|Back to top.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]

Latest revision as of 20:17, 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

Selected recent methods reports for tissue culture cells

Selected recent methods reports for in vivo


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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:

Antibodies.png

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:

Drosophila Material Resources (Reagents)

Includes:


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