Services and Pricing
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 and 'navigation' among facilities, resources, etc.
NEW in 2014: Access to genome-scale CRISPR pooled library screening through the Broad Institute Genetic Perturbation Platform (formerly RNAi Platform).
NEW in 2014: Online GESS seed sequence enrichment analysis of RNAi screen datasets. This online tool is relevant to both siRNA and shRNA screens. Post-screen analysis to detect seed sequence enrichment. An important addition to informatics-based approaches to screen validation.
NEW in 2014: Genome Engineering Production Group (GEPG) at HMS provides genome engineering construct services. Useful for development of cell lines for screens as well as for follow-up of screen results.
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.
NEW for fall 2013: Genome engineering constructs. Through one of the participating centers (DRSC), we can now offer custom TALEN and CRISPR sgRNA construct production. Useful for creating custom cell lines for screening, for post-screen validation, and much more. Competitive pricing and bulk discounts. Please visit this page for information.
Please note that you can mix-and-match—e.g., use a library from one group and an assay readout instrument at another. In fact, these are exactly the type of interactions we hoped to facilitate by joining forces.
A. Reagents for Primary Screens (siRNA, shRNA and other Reagent Libraries)
Here is an overview of the available reagent sets. See below for details & pricing.
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).
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 for more information.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 or contact a facility directly. 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.
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.
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.
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.
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.
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.
* 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.
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 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). In many cases, screen imaging projects are referred for analysis to Dr. Tiao Xie at the HMS Image Data Analysis Center (IDAC). The IDAC can provide access to open source and commercial software, as well as develop customized solutions when needed.
Statistics & Bioinformatics Support. Many of the centers have database support for screen data that includes basic statistical analysis tools. For example, the ICCB-Longwood ScreenSaver database facilitates data management and analysis for siRNA screens. We can also refer you to specific open source and commercial software packages for statistical analysis and bioinformatics, as well as to expert bioinformaticians who can provide custom support. 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.
The DRSC can provide support for our online COMPLEAT tool for analysis of screen data in the context of protein complexes, including comparison of screen data from more than one condition (e.g. treated versus untreated screen data sets).
The DRSC also developed the UP-TORR tool for up-to-date annotation of the gene-to-RNAi-reagent relationship (fly, worm, mouse and human). UP-TORR is useful to screeners for choosing the right RNAi reagent for a study and for analysis or re-analysis of RNAi data.
As a collective group, the member centers in the DF/HCC Collaborative RNAi Core are interested to provide additional support for screen data analysis and integration. Feel free to contact us about your needs.
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.
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.
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.