Difference between revisions of "FlyBase:RNAi"

From FlyBase Wiki
Jump to navigation Jump to search
 
(19 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
=Popular Resource Categories=
+
= Popular Resource Categories =
  
 
{|class="wikitable"
 
{|class="wikitable"
 
|-
 
|-
−
|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:Antibodies|Antibodies]]</big>
+
|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:ScRNA-Seq|ScRNA-Seq]]</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: Antibodies|Antibodies]]</big>||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Neuroscience|Neuroscience]]</big>
 +
|-
 +
{|class="wikitable"
 +
|-
 +
|style="text-align: center; padding: 20px;"| <big>[[FlyBase:Model_Organism_Databases|Model Organism<br/> Databases]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Images|Images]]</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> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:Papers_with_technical_advances|Papers with<br/> Technical Advances]]</big> ||style="text-align: center; padding: 20px;"| <big>[[FlyBase:GSEA|Gene Set<br/> Enrichment Tools]]</big>
 +
 
 
|}
 
|}
  
−
__TOC__  
+
__TOC__
  
 
= RNAi Design/Analysis Tools =
 
= RNAi Design/Analysis Tools =
Line 14: Line 19:
 
!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
 
|-
 
|-
−
|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
+
| [https://github.com/boutroslab/nextrnai 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
−
|-
 
−
| [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
 
 
|-
 
|-
−
|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"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
+
|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
 
|}
 
|}
 
<br/>
 
<br/>
Line 28: Line 31:
 
!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
 
|-
 
|-
−
| [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.  || Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
+
| [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
 
|-
 
|-
−
|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:"| [https://bdsc.indiana.edu/stocks/rnai/index.html 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
 
|-
 
|-
 
| [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
 
| [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
 
|-
 
|-
−
|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;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
+
|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
 
|-
 
|-
−
| [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
+
| [https://thfc.zzbd.org/en 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 <em>Drosophila</em> RNAi libraries ||style="background: #efefef;"| Vienna Drosophila Resource Center (VDRC)<br/> Vienna, Austria
+
|style="background: #efefef;"| [https://shop.vbc.ac.at/vdrc_store/ 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
  
 
|}
 
|}
Line 49: Line 52:
 
!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
 
|-
 
|-
−
|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
+
|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
−
|-
 
−
| [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
 
 
|}
 
|}
 
<br/>
 
<br/>
Line 61: Line 62:
 
!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
 
|-
 
|-
−
|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="white-space: nowrap; background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
+
|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
−
|-
 
−
|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
 
−
|-
 
−
|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
 
−
 
 
 
|}
 
|}
 
<br/>
 
<br/>
Line 78: Line 74:
 
|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
 
|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
 
|-
 
|-
−
|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
+
|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
 
|-
 
|-
−
|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
+
|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
 
|}
 
|}
  

Latest revision as of 17:03, 15 February 2024

Popular Resource Categories

All Resources CRISPR ScRNA-Seq RNAi Stocks Antibodies Neuroscience
Model Organism
Databases		 Images Maps Protocols Papers with
Technical Advances		 Gene Set
Enrichment Tools

RNAi Design/Analysis Tools

Resource Description Author/Source
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
DKFZ
Heidelberg, Germany
SnapDragon A tool for the design of long dsRNAs for specific cell-based gene knockdown in Drosophila melanogaster via an RNAi approach. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
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. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
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
National Institute of Genetics
Mishima, Japan
TRiP Transgenic RNAi Project 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 BDSC. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
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 Vienna Drosophila Resource Center (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). DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
Harvard Medical School
Boston, MA, USA


RNAi Screening Centers

Resource Description Author/Source
DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR) DRSC/TRiP Functional Genomics Resources at Harvard Medical School provides high throughput RNAi screens. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
Harvard Medical School
Boston, MA, USA


RNAi Results, Validation and Phenotypes

Resource Description Author/Source
GenomeRNAi GenomeRNAi is a database containing phenotypes from cell-based and in vivo RNA interference (RNAi) screens in Drosophila. GenomeRNAi
DKFZ
Heidelberg, Germany
RSVP RNAi Stock Validation and Phenotypes for in vivo RNAi studies. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
Harvard Medical School
Boston, MA, USA
Cell-Based RNAi Screen Summary A summary of public cell-based DRSC screens. DRSC/TRiP Functional Genomics Resources (DRSC/TRiP-FGR)
Harvard Medical School
Boston, MA, USA


  Back to top. | Back to All Resources Page. | Provide Feedback.



Retrieved from "https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:RNAi&oldid=172726"