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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.

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KI researchers Ana Munoz Manchado, Sten Linnarsson, and Jens Hjerling-Leffler. Photo: Stefan Zimmerman.

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.

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Chemical Proteomics and Proteogenomics

Chemical Proteomics & Proteogenomics (CPP) 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 and proteogenomics facility is also a node in Swedish National Mass Spectrometry Facility, BioMS.

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Chemical Proteomics Core Facility

The facility 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.

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Clinical Proteomics Mass Spectrometry

Clinical Proteomics Mass Spectrometry (MS) is a core facility that offers 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 continuously strive to develop and implement cutting edge research methods in their services. This is exemplified 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 the Stockholm county council (SLL).

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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.

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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.

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High Throughput Genome Engineering

The High Throughput Genome Engineering (HTGE) facility provides affordable access to high throughput functional genomic screens using the CRISPR/Cas9 system in cell lines. Pooled CRISPR/Cas9 screening enables parallel interrogation of thousands to tens of thousands of genes for involvement in biological processes of interest. HTGE provides access to verified lentiviral CRISPR guide libraries for whole genome and more targeted loss- and gain of function studies (CRISPR knock-out, CRISPR inhibition, CRISPR activation). They also offer generation of stable Cas9-expressing lines in users’ cells of interest.

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Karolinska Genome Engineering

The Karolinska Genome Engineering Facility (KGE) are specialists in CRISPR/Cas technology, and it is their mission to facilitate and accelerate your research by providing flexible and affordable gene-editing services in cells. Your cell type, your edit – from strategy design to delivery of a cell pool with quantified allele frequency. KGE is a branch of the High Throughput Genome Engineering, a national SciLifeLab facility (see above).

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KI Gene – Genetic Analysis

KI Gene 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.

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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.

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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.

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National Mass Cytometry 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.

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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.

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Proteomics Biomedicum

The Proteomics Biomedicum facility provides services using best available proteomics techniques and methods with focus on label-free quantitative proteomics.

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