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**This page is a work-in-progress concept of reformatting our resource and reagent list.**

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CRISPR

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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. Incorporates NAG/NGG 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. Display sgRNA sites as tracks on UCSC's genome browser, search via gene, or predict via sequence.	Giraldez Lab Yale University New Haven, USA
DRSC Find CRISPR Tool	A tool for discovering gRNA targets located throughout the Drosophila genome (release 5) using gene IDs, symbols, or chromosome locations. Allows for filtering of off-target sites and control of mis-match stringency. Incorporates NAG/NGG PAM sequence detection.	DRSC Harvard Medical School Boston, USA
E-CRISPR	gRNA genome-wide (release 5) target finder, searchable via gene symbol or sequence. Options for numerous species (fly, human, mouse, others). Offers "relaxed, medium and strict" search options. Incorporates NAG/NGG 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.	Zhang Lab MIT Boston, MA, USA
CRISPOR	To be filled.	Tefor France
CRISPR-ERA	To be filled.	Lei Stanley Qi Lab and Xiaowo Wang Lab Stanford University Standford, USA

CRISPR Stocks

Resource	Description	Author/Source
CRISPR system stocks for site-specific mutagenesis	Stocks used to express Cas9 nuclease and/or tracrRNA maternally so that chimeric RNAs (also referred to as guide RNAs) or CRISPR RNAs (crRNAs) can be injected into fly embryos to generate new mutations without the need for helper plasmids, or so that they can be used in combination with chimeric or CRISPR RNAs expressed from transgenic constructs.	Bloomington Stock Center Indiana University Indiana, USA
CRISPR Fly Design	To be filled.	MRC - Laboratory of Molecular Biology
The TRiP Toolbox Stocks	TRiP Toolbox stocks available at the BDSC. This Toolbox is the set of fly lines used to generate the RNAi transgenic lines, as well as GAL4 lines used by the TRiP that contain UAS-dicer2 to enhance the knock-down.	To be filled.

CRISPR Vectors

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.
Example	Example	Example
Example	Example	Example

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.
Example	Example	Example
Example	Example	Example

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