Fluorescence activated cell sorting in genome-scale CRISPR screening for dissection of biological pathways and intracellular signaling circuits

Name of applicant

Jacob Giehm Mikkelsen


Aarhus University


DKK 5,776,310



Type of grant

Research Infrastructure


Cells of the human body are dynamic entities that respond and adapt to the surrounding environment through intracellular signaling and regulatory circuits linked to regulation of genes in the genome. This is evident for example during virus infection, where immune cells act by initiating transcriptional programs leading to immune protection. In this project, we will utilize novel genome-wide screening approaches based on the CRISPR technology in combination with advanced fluorescence-activated cell sorting in a wide range of interdisciplinary studies. Our aim is to identify and characterize genes involved in a wide variety of cellular phenotypes, ranging from signaling during infection and cell death to responses to mechanical stretch, cancer drugs, and genetic therapies.


The capacity of our cells to develop and adapt is orchestrated by >21.000 protein-encoding genes and >6.000 RNA genes. Although we already know where these genes are located in the genome and often how they are regulated, we still don't know when they are activated and what roles they may play in different cell types and organs. It is essential therefore to push the development of methods for linking genes with specific phenotypes and describing their roles in regulatory circuits shaping the molecular behavior of cells. Based on advanced genome-wide screening methods and cellular fluorescence readouts, this project drives identification of genes facilitating hypothesis-driven research within diverse scientific subject areas including immunology, cancer, and cardiovascular diseases.


Our current high-throughput CRISPR screening pipeline includes lentiviral library design and production, cell line engineering, selection schemes and phenotypic readouts, next-generation sequencing, and bioinformatic analysis of screening sequencing data. This pipeline is fully established and is immediately available for gene identification studies. Moreover, we have established cell models allowing fluorescence to be used as a readout for relevant cellular phenotypes, including activation of immune signaling and induced cell death. With this grant, we will upgrade the infrastructure and strengthen interdisciplinarity. We will generate a genome screening network at Aarhus University ('GenomeScan at AU') offering the screening pipeline to colleagues across the AU campus and the hospital.

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