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CRISPR

Introduction

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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, 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, 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, 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 to use for the 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 Drosophila.	Addgene Cambridge, MA
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 extensive overview and resource collection for CRISPR gene editing in Drosophila.	MRC Laboratory of Molecular Biology Cambridge, UK
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

CRISPR Methods Publications

• 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] Review. PubMed PMID: 26447401.

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RNAi

Introduction

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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
UP-TORR, Updated Targets of RNAi Reagents	A lookup tool for searching TRiP, VDRC and NIG in vivo RNAi collections.	DRSC, Harvard Medical School, Boston, MA, USA

RNAi Stocks for in vivo studies (fly stocks)

Resource	Description	Author/Source
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	Relevant description	DRSC, Harvard Medical School, Boston, MA, USA
DRSC Libraries	Genome-Wide Libraries for Drosophila RNAi Screening and Validation	DRSC, Harvard Medical School, Boston, MA, USA

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
TRiP, Transgenic RNAi Project	The TRiP screening facility provides the space and equipment to carry out a complete survey of the current set of TRiP stocks.	DRSC, Harvard Medical School, Boston, MA, USA

RNAi Results, Validation and Phenotypes

Resource	Description	Author/Source
GenomeRNAi	GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila	GenomeRNAi, DKFZ, Heidelberg, Germany
[http://rnaicut.csail.mit.edu/ RNAiCut	Automated detection of significant genes from functional genomic screens	Berger Lab, MIT, Boston, MA, USA
RSVP|	RNAi Stock Validation and Phenotypes	DRSC, Harvard Medical School, Boston, MA, USA
Cell-Based Screen Summary	A summary of public DRSC screens	DRSC, Harvard Medical School, Boston, MA, USA

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Stock Centers

List of Drosophila Stock Centers

Resource	Author/Source	Additional Information
CRISPR system stocks for site-specific mutagenesis	Bloomington Stock Center	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.
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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