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Functional Genomics

This Core provides cutting-edge technology to assay gene function both in living animals and in cell culture. The Functional Genomics Shared Resource offers assistance with screening using the latest RNAi technologies and CRISPR reagents. For pricing information or other questions contact the Resource Manager, Ken Chang.

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Shared Resource Staff

Resource Head

Christopher Vakoc, M.D., Ph.D.
vakoc@cshl.edu

Director

Kenneth Chang, Ph.D.
changk@cshl.edu

Resource Technician

Kaarina Hanington
khaningt@cshl.edu

This Core offers both RNAi and CRISPR screening technology. We provide guidance, reagents, technical support, and data analysis to enable researchers to perform shRNA and CRISPR screens. Investigators interested in screening and/or obtaining reagents are encouraged to set up a consultation with Ken Chang. Services include:

  • Consultation. Initial and regular meetings to discuss the overall needs, services, and research objectives as well as optimization, and troubleshooting.
  • Genetic screens using RNAi and CRISPR libraries. Assisted pooled shRNA and CRISPR screening is offered at sub- and full-genome scale.
  • Access to shRNA clones and libraries. shRNA libraries are available for silencing gene expression in mammalian genomes.  shRNA clones are available either as individually arrayed and pooled glycerol stocks, or as purified DNA, which can be used for virus production or transfection-based assays. Focused shRNA collections to target kinase, phosphatase, epigenetic, ‘druggable’, or custom genes for human and mouse genomes are also available to researchers.
  • Access to CRISPR clones and libraries. Domain-based, pooled CRISPR libraries targeting genes of functional groups, including epigenetic, kinases, phosphatases, transcriptional factors, from human and mouse genomes, are available. The Resource will also provide the service of constructing individual sgRNA expressing clones in lentiviral vectors to investigators.
  • Virus production of shRNA and CRISPR collections
  • Design and construction of high depth custom shRNA and CRISPR libraries.  Custom shRNA libraries can be designed using the shERWOOD algorithm, which computationally predicts highly potent shRNA sequences. CRISPR sgRNAs libraries, using an algorithm designed by the Vakoc laboratory can produce negative selection phenotypes that are an order of magnitude stronger than phenotypes derived from using conventional CRISPR libraries, which are designed for mutagenesis of 5’ exons.
  • Access to shRNA and sgRNA expression vectors. The Shared Resource has Doxycycline (Dox)-inducible viral vectors for shRNA expression. A selection of constitutive promoters (EF1-Alpha, CMV, PGK, SFFV, CAGS, and MSCV-LTR) are available for gene silencing in multiple cell types. CRISPR vectors (developed by the Vakoc Laboratory) for sgRNA expression (with and without SpCas9) with different fluorescent makers, as well as SpCas9 expression vectors are also available.
  • Equipment Access. Equipment is available for screening, including: MacsQuant FACS analyzer; BIOMEK Robotic liquid handler; Perkin Elmer Enspire plate reader; Illimina Miseq sequencer; Nikon Fluorescence microscope (with z-stacking), Bio-Rad CFX96 Real time PCR system, and cell culture hoods/incubators.

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