Genetic Perturbation Platform
The Genetic Perturbation Platform (GPP) provides CBMR scientists and collaborators access to state-of-the-art large-scale genetic perturbation screening techniques.
The Genetic Perturbation Platform (GPP) provides CBMR scientists and collaborators access to state-of-the-art large-scale genetic perturbation screening techniques. These techniques leverage CRISPR technology to transduce up to thousands of guide RNAs in target cells, enabling a systematic screening of large numbers of genetic perturbations in a single experiment with single-cell transcriptomic readout.
The high-resolution multidimensional data provides information on gene and enhancer functions across the genome, helping to identify and validate disease associated gene-enhancer links and networks as well as the discovery of potential drug candidates.
GPP’s aim is to:
- Make large-scale genetic perturbation screens available for CBMR scientists and their collaborators to advance and accelerate their scientific contribution and outreach within the field of functional genomics.
- Share knowledge with the scientific community to accelerate the adoption of genetic perturbation techniques in Denmark.
- Tailored guidance on project planning.
- Assistance with gRNA design.
- Assistance with primer design for TAPseq.
- gRNA library pooling, lentivirus production and transduction
- Pooled perturbation screens with single-cell RNA readouts (in collaboration with SCOP).
- Computational support (in collaboration with SCOP)
- Access to iPS cells with inducible dCas9-KRAB.
If our services could be relevant for your research project or you want to learn more about our techniques, please send us an email at CBMR-GPP@sund.ku.dk and we will arrange a meeting.
GPP Services
Pooled Genetic Screens
GPP offer different pooled genetic screen services, which are listed below. GPP provides tailored guidance throughout a project from cell model systems and delivery strategy to gRNA design and gRNA transduction. For all single-cell RNAseq readouts, GPP collaborates closely with the Single-Cell Omics Platform (SCOP).
- Perturb-sequencing: A technique that combines CRISPRi editing system for precise gene manipulations in combination with single-cell RNA sequencing (10X Genomics) readout for whole transcriptome profiling of perturbation effects.
- Targeted Perturb-Sequencing (TAPseq): A targeted pooled genetic screening technique with a sequencing readout focusing on genes of interest instead of whole-transcriptome profiling. This technique is cost-effective and increases the sensitivity and ability to detect lowly expressed genes
Services under development
- Perturb-sequencing with sample hashing: Perturb-seq with antibody-based cell surface detection. Using cell hashing, samples can be multiplexed whereby technical viability will be reduced.
- Perturb-sequencing (enhancer-based): A pooled enhancer screens for enhancer-targeted gene profiling.
Future areas of interest:
- CRISPR activation (CRISPRa) technology for gene or enhancer based activation.
- SPEAR-ATAC: Perturbation screen with an accessibility readout using scATAC-Seq, which allow for the detection of changes in chromatin accessibility following genetic perturbations
- Large-scale genetic perturbation screens with optical phenotypic readout.
