Difference between revisions of "Resource Portal"

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| [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
 
| [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
 
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=== List of Drosophila Species Collections ===
 
=== List of Drosophila Species Collections ===

Revision as of 19:57, 8 December 2015

FlyBase maintains extensive lists of useful 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 Bioinformatic Tools

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. Incorporates PAM sequence detection. 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). Incorporates PAM sequence detection. 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. Incorporates PAM sequence detection. 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. Incorporates PAM sequence detection. DKFZ/Boutros Lab
Heildelberg, Germany
CHOPCHOP Search for gRNA targets (release 5). Flexible inputs (gene name, genomic coordinates or DNA sequence) and detection of off-target sites. Incorporates PAM sequence detection. Schier & Church Labs
Harvard University
Cambridge, MA, USA
CRISPR Design Identification of gRNA sites genome wide (release 5). Offers options for multiple species. Incorporates PAM sequence detection. 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 Stock Center
Indiana University
Indiana, USA
CRISPR Fly Design Stocks available from 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. DRSC
Harvard Medical School
Boston, MA, USA
DRSC Single Cell Cloning Protocol Single-cell cloning method useful for Drosophila cell CRISPR gene editing 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| Cell-based RNAi reagent design 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. DRSC, Harvard Medical School, Boston, MA, 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
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. BDSC, Bloomington Drosophila Stock Center, Bloomington, IN, USA
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. 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 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) 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. 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 DRSC, Harvard Medical School, Boston, MA, USA
Cell-Based RNAi Screen Summary| A summary of public cell-based DRSC screens DRSC, Harvard Medical School, Boston, MA, USA


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Stock Centers

List of D. melanogaster Stock Collections

BDRC, Bloomington Stock Center Description Author/Source
BDRC, Bloomington Stock Center The BDSC collects, maintains and distributes Drosophila melanogaster strains for research. 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. 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 National Institute of Genetics, Mishima, Japan
CRISPR system stocks for site-specific mutagenesis CRISPR system stocks for site-specific mutagenesis at BDSC Indiana University, Bloomington, IN, USA
Tsinghua Fly Center (THFC) Transgenic RNAi fly lines 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

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 on 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 can be found attached to their respective Gene Report under "Stocks and Reagents" --> "Antibody Information".
For example, the follow image is taken from the Notch gene report:

Antibodies.png


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