Functional Genomics

The DF/HCC Functional Genomics Core brings together a number of local experts, resources, and centers in the field of functional genomics to help researchers design, perform, and analyze the results of RNAi screens and CRISPR-Cas9 projects relevant to cancer study.

Understanding the mechanisms that underlie the development and progression of cancer is fundamental to finding better approaches to prevention and treatment. High-throughput RNA interference (RNAi) screening is a state-of-the-art method for large-scale investigation of gene function. CRISPR-Cas9 gene editing technologies offer complementary approaches for small and large-scale functional analysis. The Functional Genomics Core offers a single portal through which DF/HCC members can learn about RNAi and CRISPR-Cas9 services relevant to mouse, human, Drosophila and other systems.

Key Services

  • Consultation on RNAi screen and CRISPR-Cas9 engineering projects
  • Reagents for functional genomics screening (siRNA, shRNA and other reagent libraries)
    • -Pooled RNAi screening libraries—human or mouse cells
    • -Pooled CRISPR-Cas9 screening libraries—human cells
    • -Arrayed RNAi screening libraries—human cells
    • -Arrayed RNAi screening libraries—mouse cells
    • -Arrayed RNAi screening libraries—Drosophila cells
    • -Stage- and tissue-specific in vivo RNAi screening in Drosophila
    • -Reagents for miRNA interrogation (mimics and inhibitors)—human cells and Drosophila
  • Support for CRISPR-Cas9 genome engineering
    • -Access to custom CRISPR/Cas9 sgRNA services—any species
    • -Access to custom knock-in donor cassette services—and species
  • Bioinformatics support for RNAi screen and CRISPR-Cas9 projects, including
    • -Development of custom gene lists for focused screens
    • -Statistical and enrichment analysis of large-scale screen data
    • -Off-target analysis (including via our Online GESS software tool)
    • -CRISPR-Cas9 knock-out and knock-in project design
  • Automated assay read-out equipment (96-well and 384-well compatible)
    • -Luminescence and fluorescence “plate readers”
    • -Laser-scanning cytometers
    • -Epifluorescence microscopes
    • -Fluorescence confocal microscope (automated water immersion 20x, 40x, 60x)
  • Automated liquid handling robotics for screening and other studies
  • Reagents for secondary screens and follow-up studies
  • Additional reagents and resources


Pricing is set by individual participating groups. Please contact the Core Director or individual site locations for pricing information.

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.

Writing a grant that proposes an RNAi screen or the use of CRISPR-Cas9 technologies at large scale? We can help with project planning, key references, budgeting, and letters of support.

Publication Acknowledgement:

If research supported by this core facility results in publication, please acknowledge this support by including the following in your publication(s):
"We thank Dana-Farber/Harvard Cancer Center in Boston, MA, for the use of the Functional Genomics Core, which provided __________ service. Dana-Farber/Harvard Cancer Center is supported in part by a NCI Cancer Center Support Grant # NIH 5 P30 CA06516."