Difference between revisions of "FlyBase:CRISPR"

From FlyBase Wiki
Jump to navigation Jump to search
(→‎CRISPR gRNA Design Resources: Updated the DRSC tool to indicate the use of Release 6.)
Line 3: Line 3:
 
{|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: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>
 +
|-
 +
|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>
 
|}
 
|}
  
−
__TOC__  
+
 
 +
 
 +
__TOC__
  
 
= CRISPR gRNA Design Resources =
 
= CRISPR gRNA Design Resources =
Line 18: Line 22:
 
| [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 multiple species (fly, zebrafish, mouse, human, others).|| Giraldez Lab<br /> Yale University<br /> New Haven, CT, USA
 
| [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 multiple species (fly, zebrafish, mouse, human, others).|| Giraldez Lab<br /> Yale University<br /> New Haven, CT, USA
 
|-
 
|-
−
|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). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets.  ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
+
|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 6, current FlyBase release'''). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets.  ||style="background: #efefef;"| Drosophila RNAi Screening Center (DRSC)<br/> Harvard Medical School<br/> Boston, MA, USA
 
|-
 
|-
 
| [http://cas9.cbi.pku.edu.cn/ Cas9 Design] || A CRISPR/Cas9 guide RNA design tool. Support for multiple species including fly (release 5), zebrafish, mouse, human, and others. || Center for Bioinformatics<br/> Peking University<br/> Beijing, China
 
| [http://cas9.cbi.pku.edu.cn/ Cas9 Design] || A CRISPR/Cas9 guide RNA design tool. Support for multiple species including fly (release 5), zebrafish, mouse, human, and others. || Center for Bioinformatics<br/> Peking University<br/> Beijing, China
Line 98: Line 102:
 
*  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
 
*  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
 
* 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
 +
* Kunzelmann S, Böttcher R, Schmidts I, Förstemann K. [http://www.g3journal.org/content/early/2016/04/11/g3.116.028241.abstract?papetoc '''A comprehensive toolbox for genome editing in cultured Drosophila cells.'''] G3 (Bethesda). 2016 Apr 13; doi:10.1534/g3.116.028241.
  
 
= Selected recent CRISPR method reports for <em>in vivo</em> =
 
= Selected recent CRISPR method reports for <em>in vivo</em> =

Revision as of 18:34, 3 January 2017

Popular Resource Categories

All Resources CRISPR RNAi Stocks Model Organism
Databases
Antibodies Images Neuroscience Maps Protocols


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 several 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 multiple 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 6, current FlyBase release). Searchable by gene ID, symbol, or chromosome location. Includes options to modify mismatch stringency for off-targets. Drosophila RNAi Screening Center (DRSC)
Harvard Medical School
Boston, MA, USA
Cas9 Design A CRISPR/Cas9 guide RNA design tool. Support for multiple species including fly (release 5), zebrafish, mouse, human, and others. Center for Bioinformatics
Peking University
Beijing, China
CCTop CRISPR/Cas9 Target online predictor. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Notably large set of configurable parameters. Center for Organismal Studies
University of Heidelberg
Heidelberg, Germany
E-CRISP gRNA genome-wide target finder, searchable via gene symbol or sequence. Relaxed, "medium", or strict search options. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Boutros lab, DKFZ
Heidelberg, Germany
CHOPCHOP Search for gRNA targets. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Configurable options for off-targets, PAM motifs, and 5' requirements. Schier & Church Labs
Harvard University
Cambridge, MA, USA
CRISPR Design Identification of gRNA sites genome wide. Support for multiple species including Drosophila (release 5), zebrafish, mouse, human, and others. Zhang Lab
MIT
Boston, MA, USA
CRISPOR A program that helps design, evaluate, and clone guide sequences for the CRISPR/Cas9 system. Support for multiple species including several Drosophila (release 5), zebrafish, mouse, human, and others. Tefor
France


CRISPR Stocks

Resource Description Author/Source
CRISPR system stocks for site-specific mutagenesis The Bloomington Stock Center's CRISPR/Cas9 page. Includes stocks for expression of both Cas9 nuclease and tracrRNA. Bloomington Drosophila Stock Center (BDSC)
Indiana University
Bloomington, IN, USA
CRISPR Fly Design Detailed information on stocks generated by the CRISPR Fly Design group at the MRC Laboratory of Molecular Biology (available from the BDSC). MRC Laboratory of Molecular Biology
Cambridge, UK
NIG-FLY CRISPR/Cas9 Reagents, protocols, and online tools developed for genome engineering in Drosophila. NIG-FLY
National Institute of Genetics
Mishima, Japan


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
NIG-FLY CRISPR/Cas9 Reagents, protocols, and online tools developed for genome engineering in Drosophila. NIG-FLY
National Institute of Genetics
Mishima, Japan


Additional Useful CRISPR Links

Resource Description Author/Source
CRISPR Fly Design Reagents, protocols, and results from fly CRISPR/Cas9 experiments. 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
OXfCRISPR Information about protocols and reagents, new refinements of techniques, useful links to other tools, websites, and discussion groups. Liu lab
University of Oxford
Oxford, UK


Selected recent CRISPR method reviews

Selected recent CRISPR method reports for tissue culture cells

Selected recent CRISPR method reports for in vivo


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



Retrieved from "https://wiki.flybase.org/mediawiki/index.php?title=FlyBase:CRISPR&oldid=161068"