Difference between revisions of "FlyBase:RNAi"

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|style="text-align: center; padding: 15px;"| <big>[[FlyBase:External_Resources|All Resources]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:CRISPR|CRISPR]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:RNAi|RNAi]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Stocks|Stocks]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Model_Organism_Databases|Model Organism<br/> Databases]]</big>
 
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|style="text-align: center; padding: 20px;"| <big>[[FlyBase:Antibodies|Antibodies]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Images|Images]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Neuroscience|Neuroscience]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Maps|Maps]]</big> ||style="text-align: center; padding: 20px;"| <big>[http://www.flyrnai.org/tools/protocols/web/ Protocols]</big>
 
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= RNAi Design/Analysis Tools =
 
= RNAi Design/Analysis Tools =
  
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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"| [http://www.dkfz.de/signaling/e-rnai3/ E-RNAi]||style="background: #efefef; white-space:"| 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. Support for multiple species including <em>Drosophila</em> (release 5), mouse, human, and others.||style="background: #efefef;"| Boutros lab<br/> DKFZ<br/> Heidelberg, Germany
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|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
 
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| [http://b110-wiki.dkfz.de/confluence/display/nextrnai/NEXT-RNAi NEXT-RNAi] || Software for the design and evaluation of genome-wide RNAi libraries. It 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<br/> DKFZ<br/> Heidelberg, Germany
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| [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
 
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|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 <em>Drosophila melanogaster</em> via an RNAi approach. ||style="background: #efefef; white-space: nowrap"| DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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= RNAi Stocks for <em>in vivo</em> studies (fly stocks) =
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= RNAi Stocks for in vivo studies (fly stocks) =
  
 
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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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| [http://www.flyrnai.org/up-torr/ UP-TORR, Updated Targets of RNAi Reagents] || A lookup tool for searching BDSC, TRiP, VDRC and NIG-FLY <em>in vivo</em> RNAi collections.  || DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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| [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
 
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|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; 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
 
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| [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/> National Institute of Genetics<br/> Mishima, Japan
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| [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
 
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|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 correspond to orthologs of human-disease-associated genes. The stocks can be obtained from the [http://flystocks.bio.indiana.edu/ BDSC]. ||style="background: #efefef;"| DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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| [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
 
| [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
 
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|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 <em>Drosophila</em> RNAi libraries ||style="background: #efefef;"| Vienna Drosophila Resource Center (VDRC)<br/> Vienna, Austria
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|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
 
 
 
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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:"| [http://fgr.hms.harvard.edu/drsc-20-genome-wide-screening-library DRSC Libraries]||style="background: #efefef; white-space:"| Genome-wide libraries for cell-based RNAi screening and validation (on-site or shipped). ||style="background: #efefef;"| DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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| [http://www.dkfz.de/signaling/ Division of Signaling and Functional Genomics] || Genome-wide libraries for cell-based RNAi screening and validation. Includes the resource site [http://www.genomernai.org/ GenomeRNAi]. || Boutros lab<br/> DKFZ<br/> Heidelberg, Germany
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| [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
 
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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"| [http://fgr.hms.harvard.edu/fly-cell-based-rnai DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)]||style="background: #efefef; white-space:"| DRSC/TRiP Functional Genomics Resources at Harvard Medical School provides high throughput RNAi screens. ||style="white-space: nowrap; background: #efefef;"| DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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|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<br/> New York, NY, USA
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|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
 
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|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 <em>Drosophila</em> cells. ||style="background: #efefef;"| SRSF<br/> University of Sheffield<br/> Boston, MA, USA
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|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
 
 
 
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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"| [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 <em>Drosophila</em>. ||style="background: #efefef;"| GenomeRNAi<br/> DKFZ<br/> Heidelberg, Germany
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|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
 
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|style="nowrap;"| [http://fgr.hms.harvard.edu/rsvp RSVP] || RNAi Stock Validation and Phenotypes for in vivo RNAi studies. || DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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|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;"| DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)<br/> Harvard Medical School<br/> Boston, MA, USA
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|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
 
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&nbsp; [[#top|Back to top.]] | [[FlyBase:External_Resources#top|Back to All Resources Page.]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
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&nbsp; [[#top|Back to top.]] | [[External_Resources#top|Back to External Resources Page]] | [http://flybase.org/cgi-bin/mailto-fbhelp.html Provide Feedback.]
  
 
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Revision as of 15:38, 16 December 2015

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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