From genetic perturbation to biological discovery

As a national SciLifeLab Infrastructure Unit based at Karolinska Institutet, we work as collaborative scientific partners with research teams across Sweden and internationally. We co-design experiments, engineer custom cell models through precision genome editing, and perform state-of-the-art functional genomics screens to enable discoveries that would otherwise be difficult or impossible.

Whether you need a robust, high-quality fee-for-service workflow or in-depth technological co-development, CFG can tailor its expertise and infrastructure to your research question.

Core Capabilities & Technologies

Our infrastructure is built around two complementary capabilities:

1. Massively Parallel Pooled CRISPR Screening

Interrogate dozens to tens of thousands of genes or genetic elements in parallel using unbiased genome-wide screens or focused, hypothesis-driven libraries.

Genetic perturbation at scale

We perform a broad range of CRISPR-based perturbations, including:

• Loss-of-function screens: gene knockout and transcriptional repression (CRISPRi)
• Gain-of-function screens: transcriptional activation (CRISPRa)
• Mutagenesis screens: tiling mutagenesis of protein-coding genes and regulatory elements, including enhancers, promoters, UTRs, and other functional regions

Diverse phenotypic readouts

Choose readouts matched to your biological question, including:

• Survival and cellular fitness
• FACS-based phenotypic selection
• Perturb-seq and CROP-seq (single-cell transcriptomic readout)
• Cell morphology and other imaging-based phenotypes including spatial transcriptomics (optical pooled screening, in development).

Custom and off-the-shelf guide libraries

Our screening libraries incorporate Random Sequence Labels (RSLs) to increase statistical power and enable lineage tracing.

We provide ready-to-use genome-wide libraries for:

• CRISPR knockout
• CRISPRi
• CRISPRa

We also design, clone, and package bespoke lentiviral libraries for Cas9, Cas12a, Cas13b, and Cas13d, tailored to specific genes, pathways, genetic elements, or experimental models.

Model systems

Our screening capabilities span:

• Human and mouse cell lines for large-scale screens
• Primary cells and stem cells for smaller-scale screens
• In vivo screening in mouse models

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2. Precision Genome Engineering

We provide flexible, custom gene-editing solutions in human and non-human cell lines, as well as selected primary-cell and stem-cell models.

A full-spectrum genome-editing toolbox

Our methods include:

• Indel-based editing
• Targeted deletions
• Homology-directed repair (HDR)
• Base editing
• Prime editing

These approaches can be used to generate precise knockouts, knock-ins, point mutations, reporter tags, and other targeted genomic modifications.

Integrated editing workflow and analytics

We provide an end-to-end workflow covering:

1. Experimental strategy and guide design
2. Transient delivery using Neon NxT electroporation
3. Direct quantification of editing efficiency using droplet digital PCR (ddPCR) and/or in-house nanopore sequencing
4. Single-cell FACS sorting
5. Clone expansion
6. Genotyping and validation

This integrated approach enables efficient progression from experimental design to validated engineered models

Workflow precision editing projects.

Cross-facility collaborations

• CFG works closely with complementary SciLifeLab and university infrastructures to extend the scope of genome engineering projects:
• Chemical Biology Consortium Sweden (CBCS) for reporter cell-line generation for chemical screening and to investigate the mechanism-of-action of small compounds.
• The Chemical Proteomics Unit to investigate the mechanism-of-action of small compounds
• The National Genomics Infrastructure (NGI) for NGS, single cell library preparation, and Element Aviti24 spatial workflows
• The In Situ Sequencing Unit for optical pooled screening
• Karolinska Center for Transgene Technologies (KCTT) for mouse model development
• Lund University Cell and Gene Therapy Core for iPSC applications

What can you achieve?

Engineer custom cell models

Generate precisely engineered knockout, knock-in, point-mutant, reporter, and other cell models for functional validation, mechanism-of-action studies, and disease modelling.

Discover targets and genetic dependencies

Identify essential genes, synthetic lethal interactions, drivers or suppressors of a phenotype of interest, and other context-specific genetic dependencies across cell types, disease states, or experimental conditions.

Map drug–target interactions

Use high-resolution base-editing and scanning mutagenesis approaches to map functional protein domains, critical residues, and potential drug-binding sites at amino-acid resolution.

Dissect biological pathways

Systematically identify genetic regulators of reporter activity, protein stability, cellular phenotypes, and other biological processes. Combine CRISPR perturbations with single-cell transcriptomics and other high-dimensional readouts to resolve complex biological mechanisms.

From experimental design to biological insight

CFG can support projects across the entire experimental workflow – from strategy development and reagent design to genome engineering, screening, data generation and data analysis.

Through close collaboration with complementary SciLifeLab infrastructures, we can help integrate CRISPR-based approaches with chemical biology, proteomics, genomics, single-cell technologies, and bioinformatic analysis

Practical Information

CFG is an academic, non-profit national infrastructure unit open to researchers in academia, healthcare, and industry across Sweden and internationally.

Start with a consultation!

We offer an initial project consultation at no charge. CFG experts can assess experimental feasibility, discuss appropriate technologies and workflows, and provide a project-specific quotation. Whether you need a standard fee-for-service workflow or are looking for custom technological development, contact us to discuss your project and receive a tailored proposal. 

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