Karolinska High Throughput Center (KHTC)

National facility


KHTC is a core facility with an extensive collection of state-of-the-art instrumentation and research tools for functional genomics studies, including integrated liquid and microplate handling, high-throughput screening (HTS) and Next Generation Sequencing (NGS) capabilities. The facility is among the most advanced centers of its kind in Europe and has now implemented pooled CRISPR/Cas9 screening for large scale genome editing studies. In addition, we provide services in the fields of systems biology and drug-discovery to the Swedish and international scientific community. KHTC operates as an investigator-assisted facility, where user training in experimental design and operation of the instruments is an important part. In association with the infrastructure, KHTC provides access to research tools including CRISPR guide RNA libraries, genome-wide siRNA libraries, human ORFeome clones, annotated sets of drugs and the diverse SciLifeLab compound collection.


  • Genome Editing: pooled CRISPR/Cas9 screening followed by NGS readout and initial data analysis.
  • Assay: miniaturization, optimization and validation from 96- to 384- or 1536-well formats.
  • HTS: screening of siRNAs or compounds in biochemical and cellular assays including follow up of knock-down efficiency or hit-validation.
  • Liquid handling: from nl acoustic dispensing of DMSO solutions to multiwell cell seeding and washing.
  • Training: experimental design and operation of the high-throughput laboratory platforms.


The equipment is set up in technological platforms:

  • Automated liquid and multiwell-plate handling platforms (Beckman FxP-based)
  • Biochemical and cellular analysis platform (Thermo Scientific Orbitor-based)
  • High-throughput flow cytometry platform with integrated auto-sampler system (Intellicyt HyperCyt)
  • High-capacity platform for analysis of biomolecular interactions (Agilent Bravo and BechCel).
  • Microbial colony picking and arraying instrument (Molecular Devices QPix).

Our detection instruments include:

  • Automated microscope: Pathway 855 from BD Biosciences.
  • High-content imager: Acumen eX3 from TTP Labtech.
  • Flow cytometer; CyAn ADP from Beckman.
  • Multilabel plate reader; EnVision from PerkinElmer.
  • Real-time PCR device; LightCycler 480 from Roche.
  • NGS sequencers; HiSeq2000 and 4000 from Illumina.


Activities at KHTC include but are not limited to the following applications:

  • Large-scale functional genomics studies using CRISPR/Cas9 and RNA interference (RNAi).
  • Automated chemical compound HTS for drug discovery and chemical genetics studies.
  • High-content microscopy and flow cytometry.
  • High-capacity Systematic Evolution of Ligands by Exponential Enrichment (SELEX).
  • Chromatin immunoprecipitation followed by sequencing (ChIP-seq).


  • During 2015, KHTC assisted 51 principal investigators and completed 64 projects.
  • We have assisted scientists from four Swedish universities, several international universities and small biotech companies.
  • Results generated at KHTC have been incorporated into 23 publications, 7 of these have been published in journals with impact factor >25.