Researchers are encouraged to contact the Core Coordinator at any stage of the screening process, from assay development to data analysis, for confidential advice on your project. Writing a grant that proposes a screen? We can also help with advice, key references, budgeting for a screen, and letters of support. Below are listed the various RNAi reagent libraries, equipment, and related services available from the member groups.

Please note that you can "mix-and-match" reagents and equipment available at or from different groups—for example, use a library from one group and an assay readout instrument at another. In fact, these are exactly the type of interactions the participating groups hope to facilitate by joining forces.

A. Reagents for Primary Screens (siRNA, shRNA and other Reagent Libraries)

1. Pooled RNAi Screening Libraries—Human or Mouse Cells

2. Arrayed RNAi Screening Libraries—Human Cells

3. Arrayed RNAi Screening Libraries—Mouse Cells

4. Arrayed RNAi Screening Libraries—Drosophila Cells

5. RNAi Screening in whole animals in Drosophila

NEW in 2010: Reagents for miRNA interrogation

B. Reagents for Secondary Screening and Follow-Up

C. Assay Read-Out Equipment

D. Additional Equipment

E. Image Analysis, Statistics & Bioinformatics Support for Screen Data Analysis

F. Cell Lines

G. Additional Reagents & Resources

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A. Reagents for Primary Screens (siRNA, shRNA and other Reagent Libraries)

NOTE: Individual shRNA plasmid constructs are available from the DF/HCC DNA Resource Core. Please see their PlasmID website.

Here is an overview of the available reagent sets. See below for details & pricing.

Assay Format	Cells	Coverage	Reagent Type	Center(s)
Pooled	Any Human or Mouse Cell Type	Full-Genome	shRNA (lentivirus)	Various
Arrayed	Transfectable Human and Mouse Cells	Full-Genome and Sub-Sets	siRNA	ICCB-Longwood
Arrayed	Any Human or Mouse Cell Type	Full-Genome and Sub-Sets	shRNA (lentivirus)	Various
Arrayed	Primary & Cultured Drosophila Cells	Full-Genome and Sub-Sets	dsRNA	DRSC

Detailed Information about the Libraries, Assay Read-Out Instruments, and other Services & Equipment Available

New in 2010: Two collections of miRNA mimics and one collection of miRNA inhibitors for human cell screening (through ICCB-L; see their library page).

1. Pooled RNAi Screening Libraries—Human or Mouse Cells

a. Elledge Lab Pooled Libraries. Pooled shRNA libraries described in the following publications are available from Steve Elledge’s lab.  Please contact the Core Coordinator or contact the Elledge lab directly to make a request (DNA or glycerol). These pools are also available in experiment-ready viral form. The viral preps are done at the Harvard Institute of Proteomics and are associated with a viral prep fee.  Please contact the Core Coordinator for more information and pricing.

Pools available from the Elledge group are those described in:

Silva et al. (2005) Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37:1281-8.
Schlabach et al. (2008) Cancer Proliferation Gene Discovery Through Functional Genomics. Science 319:620.
Silva et al. (2008) Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319:617-20.

b. Pooled Mouse or Human Libraries from The RNAi Consortium (TRC). TRC libraries are available in pooled format (in addition to arrayed format; see below) at the DFCI RNAi Facility and the RNAi Platform of the Broad. For more information and pricing, please contact the Core Coordinator.

Described in:

Moffat et al. (2006) A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen. Cell. 124(6):1283-1298.
Luo et al. (2008) Highly parallel identification of essential genes in cancer cells. PNAS. 105(51):20380–20385.

2. Arrayed RNAi Screening Libraries—Human Cells

Arrayed Human siRNA Libraries. Please see ICCB Longwood Screening Facility RNAi Libraries for up-to-date information about the arrayed siRNA libraries available at the ICCB-Longwood Screening Facility. Note that on the ICCB-L website, some siRNA reagents are referred as "pools" because each well in the arrayed library contains a small pool of siRNAs directed against a single target gene.

Arrayed Human shRNA Libraries. Please see The RNAi Consortium (TRC) for an overview of the arrayed TRC shRNA (lentiviral) libraries, which are available at the DFCI RNAi Facility and the RNAi Platform at the Broad Institute.

3. Arrayed RNAi Screening Libraries—Mouse Cells

Arrayed Mouse siRNA Libraries. Please see ICCB Longwood Screening Facility RNAi Libraries for up-to-date information about the arrayed siRNA libraries available at the ICCB-L Screening Facility. Note that on the ICCB-L website, some siRNA reagents are referred as "pools" because each well in the arrayed library contains a small pool of siRNAs directed against a single target gene.

Arrayed Mouse shRNA Libraries. Please see The RNAi Consortium (TRC) for an overview of the arrayed TRC shRNA (lentiviral) libraries, which are available at the DFCI RNAi Facility and the RNAi Platform at the Broad Institute.

4. Arrayed RNAi Screening Libraries—Drosophila Cells

The DRSC has designed, generated and maintains full-genome and additional RNAi libraries for screening (in some cases, in collaboration with other groups). The full-genome library is available for screening on-site at the DRSC and additional libraries are available for screening on- or off-site.

Related information:

DRSC dsRNA Libraries for RNAi Screening
DRSC Library Costs

5. RNAi Screening in whole animals in Drosophila

For information about availability of fly strains for tissue-specific expression of RNAi hairpins (Gal4-UAS system), please see the Transgenic RNAi Project web site.

B. Reagents for Secondary Screening and Follow-Up

After a large-scale primary screen, the next step is usually to verify results using the same and/or additional RNAi reagents directed against the same target genes that "hit" in the primary screen. Doing one to three replicates in the primary screen is typical but doing more replicates is recommended for secondary analysis. In general, the choice of reagents appropriate for secondary analysis reagents will be specific to the library and/or assay used in the primary screen. In some cases, however, it might be appropriate to get reagents from more than one group for follow-up (such as siRNAs from one group and shRNAs from another), particularly if you will switch cell-types as part of your secondary analysis. A number of reagents for follow-up are available from the participating groups. Please contact the core coordinator or the group that provided the library used in the primary screen for more information.

C. Assay Read-Out Equipment

Instrument	Use	Location*
Molecular Devices Analyst GT	Plate-Reader (GFP, FITC, Luciferase)	DRSC (NRB)
PE Packard Fusion	Plate-reader (Fluorescence, Luciferase, FRET, AlphaScreen etc.)	RNAi Platform of the Broad Institute
PerkinElmer EnVision	Plate-Reader (GFP, FITC, Luciferase)	DFCI RNAi Facility
PerkinElmer EnVision	Plate-Reader (GFP, FITC, Luciferase)	ICCB-Longwood (Seeley Mudd)
PerkinElmer EnVision	Plate-Reader (GFP, FITC, Luciferase)	ICCB-Longwood (Seeley Mudd)
PerkinElmer EnVision	Plate-Reader (GFP, FITC, Luciferase, SureFire/Alpha)	ICCB-Longwood (Seeley Mudd)
PerkinElmer EnVision	Plate-Reader (GFP, FITC, Luciferase, SureFire/Alpha)	RNAi Platform of the Broad Institute
MDS SpectraMax	Plate-Reader (190 to 850 nm)	DFCI RNAi Facility
MDS SpectraMax	Plate-Reader	ICCB-Longwood (Seeley Mudd)
Molecular Devices Flexstation III	Plate-Reader with Liquid Handling Automation	ICCB-Longwood (Seeley Mudd)
LiCor Aerius	Far-Red Plate Reader for In-Cell Western	DRSC (NRB)
Blueshift Isocyte	Laser scanning cytometer (488 and 532 nm)	ICCB-Longwood (Seeley Mudd)
TTP LabTech Acumen X3	Laser scanning cytometer	RNAi Platform of the Broad Institute
Applied Precision cellWoRx	High-throughput, high-content imaging	ICCB-Longwood
MDS ImageXpress	High-throughput, high-content imaging	ICCB-Longwood (Seeley Mudd)
MDS ImageXpress	High-throughput, high-content imaging	DRSC (NRB)
PerkinElmer Evotec Opera	High-throughput, high-content confocal imaging	DRSC (NRB)

* Note that purchase, service, etc. for some of the instruments may be costs that are shared among various groups. All require appropriate training and sign-up for use.

D. Additional Equipment

Equipment	Location
Cell Culture Hoods (BL2)	All Locations
Cell Culture Incubators (BL2)	All Locations
Plate Washers & Aspirators	All Locations
Liquid handling Robotics	All Locations
Cell Culture Hoods (BL2+)	DFCI, RNAi Platform at Broad

E. Image Analysis, Statistics & Bioinformatics Support for Screen Data Analysis

We encourage potential screeners to think about data and image analysis early in the process, as simple changes to assay design might have a profound influence on downstream analysis steps.

Image Analysis Support. Most of the screening microscopes (see above) come with their own software for image analysis. We can also provide access to other software programs and experts. For projects requiring a significant degree of expert input and/or customization, it can be appropriate for these expert(s) to become collaborators (i.e. co-authors).

Currently available image analysis software includes the following:

Freely available packages such as NIH Image, ImageJ and CellProfiler. Commercial packages inlcuding MDS MetaExpress (typically used with MDS ImageXpress data) and PerkinElmer Acapella (typically used with PE Opera data). Customized analysis solutions in Definiens Developer. And customized analysis solutions in MatLab. In addition, we are investigating support of image data management via OMERO (open source) and commercial derivatives.

Statistics & Bioinformatics Support. Similarly, we can refer you to specific custom and commercial software packages for statistical analysis and bioinformatics. And to experts who can craft screen-specific solutions. For projects requiring a significant degree of expert input and/or customization, it can be appropriate for these expert(s) to become collaborators (i.e. co-authors). Please contact the core coordinator for a list of current software packages available at various locations, and/or for an introduction to an appropriate image or data analyst who might be able to help with your project.

F. Cell Lines

Cell lines for Drosophila screening can be requested from the DRSC. We can also help with set-up for large-scale collection of embryos for primary cell screens.

Cell lines for mammalian screening are available from vendors such as ATCC. Please contact the core coordinator for advice on selecting the appropriate cell line(s) for your screen assay.

G. Additional Reagents and Resources

Transfection Reagent Testing Set. Want to transfect siRNAs into your favorite cell line(s) but not sure which transfection reagent is the best for the cell type(s)? The ICCB-Longwood Screening Facility has available a testing set of more than 30 different transfection reagents.

Individual shRNAs as virus. The Harvard Institute of Proteomics is in a pilot phase offering viral preps for small gene sets, based on TRC shRNAs. Please contact the core coordinator for more information.

Looking for something else? Please feel free to send us feedback on additional resources, test sets, reagent libraries or other services that the participating groups could provide, either individually or through our collaborative efforts.