Omics and high-throughput

On this page we have collected core facilities and resources within proteomics and genomics and related techniques located at our two main campuses. Several of the listed core facilities are also a part of the national research facility SciLifeLab.

DNA code and helix
Illustration by Gerd Altmann, downloaded from Pixabay, CC0.

Bioinformatics and Expression Analysis

The core facility for Bioinformatics and Expression Analysis (BEA) is a national genomic service facility located at the the Department of Biosciences and Nutrition at KI South Campus Flemingsberg. BEA provides an extensive repertoire of genomic technologies to ongoing research projects principally at the Karolinska Institute but also at other Swedish universities. This includes services for genomic analysis based on the Affymetrix, Agilent, Illumina and ABI platforms for microarrays, sequencing and qPCR. The services of BEA are extensive and ranges from experimental planning to bioinformatic support. We are also offering services for RNA and DNA purification, nucleic acid quality control and different qPCR based assays. This facility is available through the KI contact portal for core facilities in iLab.

Chemical Proteomics

Chemical Proteomics is a national facility that offers state-of-the art mass spectrometry-based proteomics support to the Swedish research community. The facility also offers expert support in experimental planning, MS-analysis and data analysis related to proteogenomics and chemical proteomics. The activities are shared between two sites in Stockholm: one at SciLifeLab and one at Karolinska Institutet. The chemical proteomics facility is also a node in Swedish National Mass Spectrometry Facility, BioMS.

Chemical Proteomics Core Facility

The Chemical Proteomics Core Facility (ChemProt) is located at Biomedicum, Campus Solna, and specializes in supporting target identification and validation, keys and bottlenecks of drug discovery and development. It is also connected to the Chemical Proteomics and Proteogenomics node at SciLifeLab. This facility is available through the KI contact portal for core facilities in iLab.

Clinical Genomics

The unit Clinical Genomics Stockholm provides a dedicated research infrastructure for projects utilizing massively parallel / next generation sequencing technologies. The unit serves as a competence center assisting the translation of genomics-based tools to routine clinical care. All projects are carried out in close collaboration with the Swedish healthcare system and medical expertise provided by the clinical diagnostic laboratories and patients’ managing physicians. The facility is managed within the SciLifeLab research cluster.

This facility is available through the KI contact portal for core facilities in iLab.

Clinical Proteomics Mass Spectrometry

Clinical Proteomics Mass Spectrometry (MS) is a core facility that offers you an opportunity to analyze the proteome composition of biological samples. The facility provides expertise and services in a wide range of MS-based proteomics methods with focus on in-depth quantitative proteomics and clinical proteomics. The facility also offers expert support in experimental design as well as downstream data analysis to ensure a high quality service.

The team behind this facility strive to develop and implement cutting edge research methods in our services. This is exemplied by the level of data produced by the HiRIEF method used for in-depth proteomics, and by our continuous development of bioinformatics methods for optimal use of the generated data. The financial support for the facility is provided by Region Stockholm (the county council).  This facility is available through the KI contact portal for core facilities in iLab.

CRISPR Functional Genomics

At CRISPR Functional Genomics (CFG), we are specialists in functional genomics applications of CRISPR technology. Our sister facility, Karolinska Genome Engineering (KGE), focuses on precision genome editing in cell lines, as well as on reagent design for creating mouse strains. Together, CFG and KGE form the CRISPR Center Sweden and cover the entire range of CRISPR applications, from the creation of knock-out/knock-in cell models to massively parallel, genome-wide perturbation screens.

We strive to make the latest technological innovations available to the Swedish research community as quickly as possible. Examples of our toolbox include base-editing, prime-editing, pooled CRISPR loss- and gain-of-function screens, and coupling pooled screens with single cell transcriptomics. One emerging focus area is target identification and mode-of-action elucidation, which we pursue in collaboration with the Chemical Biology Consortium Sweden and the Chemical Proteomics unit  at SciLifeLab.

This facility is available through the KI contact portal for core facilities in iLab under the collegive name CRISPR Center Sweden.

Eukaryotic Single Cell Genomics

The Eukaryotic Single Cell Genomics facility aims at providing single cell transcriptomics and genomics services to the scientific community. Single cell analysis is an emerging technology that allows for the exploration of the transcriptome and genome content of individual cells. The facility offers streamlined single-cell RNA sequencing as well as whole genome DNA amplification to the scientific community in Sweden and beyond. The facility is of national interest and part of the SciLifeLab. This facility is available through the KI contact portal for core facilities in iLab.

Genomic Medicine Center Karolinska

Genomic Medicine Center Karolinska (GMCK) is a KI/SLL core facility for translational research, clinical trials and diagnostics, focusing on transitioning of next generation sequencing (NGS) from basic science to clinical diagnostic settings. The facility supports KI and KS researchers and clinical users in aspects covering experimental design, data generation, data analysis and solutions for clinical decision support.

The facility is operates as a joint unit between the Clinical Genomics facility at SciLifeLab and a genomics unit at Karolinska university laboratory When applicable, the facility will support researches by facilitating the contact with other genomics and high-throughput facilities at KS(/SLL), KI and Scilifelab. This facility is available through the KI contact portal for core facilities in iLab under the name Clinical Genomics Unit.

Karolinska Genome Engineering

At Karolinska Genome Engineering Facility (KGE), we are specialists in precision editing in cell lines and iPSCs using CRISPR technology. Our sister facility, CRISPR Functional Genomics (CFG) focuses on functional genomics applications of CRISPR technology, such as genome-wide or custom genetic screens. Together, KGE and CFG for the CRISPR Center Sweden and cover the entire range of CRISPR applications, from the creation of knock-out/knock-in cell models to massively parallel, genome-wide perturbation screens.

We strive to make the latest technological innovations available to the Swedish research community as quickly as possible. Examples of our toolbox are base-editing, prime-editing, pooled CRISPR loss- and gain-of-function screens, and coupling pooled screens with single cell transcriptomics. One emerging focus area is target identification and mode-of-action elucidation, which we pursue in collaboration with the Chemical Biology Consortium Sweden and the Chemical Proteomics unit at SciLifeLab.

This facility is available through the KI contact portal for core facilities in iLab under the collegive name CRISPR Center Sweden.

KIGene – Genetic Analysis

KIGene offers Sanger DNA sequencing with fast turn-around time, gene expression analysis and analysis of genetic variations including SNPs, microsatellite markers and insertion/deletion polymorphisms. This facility is available through the KI contact portal for core facilities in iLab.

KI Small Molecule Mass Spectrometry Core Facility

The KI Small Molecule Mass Spectrometry (KI-SMMS) Core Facility provides analytical services using best available mass spectrometry methods with a focus on quantitative measurements of small molecules. The facility assists in designing experiments, including a broad range of samples preparation methods, in combination with generation of high-quality mass spectrometric data as well as data analysis and interpretation. This facility is available through the KI contact portal for core facilities in iLab.

Laboratories for Chemical Biology

Laboratories for Chemical Biology (LCBKI) is a KI core facility and a part of the gouvernment-funded Chemical Biology Consortium Sweden (CBCS) and SciLifeLab. The facility comprises compound handling labs, hosting the SciLifeLab compound collection of about 200 000 molecules. It also offers screening labs such as microtiter format liquid handling robotics and a wide range of plate readers, as well as chemistry labs with equipment and instrumentation for organic chemistry synthesis and analysis. This facility is available through the KI contact portal for core facilities in iLab.

Mutation Analysis Facility

The purpose and mission of the Mutation Analysis core Facility (MAF) is to help scientists at Karolinska Institutet, its associated hospitals, and other academic institutions to perform genetic, epigenetic and genetic-epidemiological research in order to identify and assess genetic factors involved in different disease processes. The facility offers techniques for targeted DNA methylation, genome-wide DNA methylation, genome-wide genotyping, targeted SNP genotyping as well as genome-wide expression analysis.

Protein Science Facility

The Protein Science Facility (PSF) provide users with protein production services and access to the state-of-the-art infrastructure for Macromolecular X-ray crystallography (MX) and biophysical protein characterization available at the Department of Medical Biochemistry and Biophysics (MBB). PSF is a National Facility for protein production within SciLifeLab and SWEDSTRUCT. This facility is available through the KI contact portal for core facilities in iLab.

Proteomics Biomedicum

The Proteomics Biomedicum facility provides services using best available mass spectrometry-based proteomics techniques and methods with focus on quantitative proteomics, including single cell proteomics. We help designing experiments, providing a broad range of efficient samples preparation methods, high quality mass spectrometric data as well as data analysis and interpretation. This facility is available through the KI contact portal for core facilities in iLab. This facility is available through the KI contact portal for core facilities in iLab.

SciLifeLab Cellular Immunomonitoring Facility

This facility provides state-of-the art Mass Cytometry analysis to the entire Swedish research community. The facility belongs to the Affinity proteomics platform within SciLifeLab and consists of two nodes, one in Stockholm and one in Linköping. Together they perform standardized Mass Cytometry experiments on customer provided samples using validated panels of metal-coupled antibodies. They also perform technology development of new experimental assays and reagents as well as novel data analysis tools. This facility is available through the KI contact portal for core facilities in iLab.

Single Cell Core Facility Flemingsberg

The main goal of the Single Cell Core Facility (SICOF) is to provide expertise and experimental support on single cell technologies for researchers at Karolinska Institutet — starting with advice on experimental setup and selection of available technology leading all the way up to delivery of clustered single cell data in a format that can be explored by researchers without the need for specialized bioinformatics expertise. The core facility is situated at our South campus area in Flemingsberg. This facility is available through the KI contact portal for core facilities in iLab.

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