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High Throughput Genome Engineering (HTGE)

New national facilities from 2017

HTGE is the foremost competence centre for CRISPR-Cas9 technology in Sweden, supporting and developing any kind of high-throughput CRISPR-Cas application.

HTGE's core service are pooled, lentiviral 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 creates and provides access to verified lentiviral CRISPR guide libraries for whole genome or targeted loss- and gain of function studies (CRISPR knock-out, CRISPR inhibition, CRISPR activation).

We also offer generation of stable Cas9-expressing lines in users’ cells of interest. We aim to keep our services cutting-edge and are always happy to implement new screening technologies in collaboration with our clients.


Workflow of a pooled screen. Phenotypic selection is performed by the client, either in their own lab or at HTGE's premises in Biomedicum. All other steps are performed by HTGE.


Your project is out of the box? All the better, we would love to hear from you!


From left to right: Soniya, Jenna, Bernhard, Georgia, Allegra. Photo: Christos Coucoravas

HTGE uses guides barcoded with random sequence labels (RSLs) in all screens. This increases increases precision and accuracy of CRISPR-Cas9 screens  (B Schmierer, SK Botla et al., 2017). PDF. Full text.

Cartoon comparing pooled CRISPR screening with (right) and without (left) random sequence labels.


Highly multiplexed CRISPR-Cas9 perturbations with single-cell RNASeq readout (CRISPR-scRNASeq).

Together with Eukaryotic Single Cell Genomics (ESCG), we offer a modified version of the Perturb-Seq approach (Replogle et al., 2016) to screen small CRISPR libraries using single cell transcriptomes as readouts.

Highly multiplexed CRISPR-Cas9 perturbations with single-cell RNASeq readout (CRISPR-scRNASeq). Hundreds of guides are synthesized as oligos, cloned in pool into a lentiviral plasmid, packaged and transduced into Cas9 expressing cells in pool. Single cells are then isolated and their transcriptomes, including the identity of the guide RNA present in each cell, are recorded. Example shown is for WT Cas9 and gene knock-out, an identical workflow is being set up for gene activation.


Our local branch, Karolinska Genome Engineering (KGE), performs precision edits in cell lines, such as knock-out, knock-in, deletions, point mutations, etc. KGE collaborate with the Karolinska Center for Transgene Technologies (KCTT) to offer CRISPR technology in mouse, and has a common pipeline with the iPSC core facility for precision editing of iPSCs.


  • Generation of Cas9-expressing cell lines, constitutive or inducible, dCas9, nCas9, Cas12a, etc.
  • High throughput pooled CRISPR screens from screen design to gene hit list
  • CRISPR-KO and CRISPR-inhibition (loss of function); CRISPR-activation (gain of function)
  • Experienced support for screen design
  • Design and production of genome-wide or custom-made lentiviral CRISPR guide libraries
  • Library transduction - all viral work carried out at HTGE
  • Preparation of genomic DNA and NGS library
  • Next generation sequencing NGI Stockholm
  • Data analysis and generation of a ranked list of hit genes
  • Multiplexed CRISPR-Cas9 perturbations with single-cell RNASeq readout (compatible with CRISPR-KO, CRISPR-i or CRISPR-a experiments)


  • Screens in cell lines, stem cells or primary cells
  • Determine essential genes in specific cell types
  • Screen for drug resistance/sensitivity genes
  • Find novel genes/pathways involved in differentiation
  • Map novel genes/pathways regulating a reporter gene
  • Pooled screening is extremely versatile; any phenotype that allows cell separation can be queried!


A Regulatory Role for CHD2 in Myelopoiesis

FS Varnoosfaderani, A Palau, W Dong, J Persson, M Durand-Dubief, JP Svensson, A Lennartsson. Epigenetics 1-13 2020 Jan 10. PMID: 31900031 DOI: 10.1080/15592294.2019.1710913

CRISPR-Cas9 Genome Editing Induces a p53-mediated DNA Damage Response

E Haapaniemi, SK Botla, J Persson, B Schmierer & J Taipale. Nature Medicine 24 (7), 927-930 Jul 2018. PMID: 29892067 DOI: 10.1038/s41591-018-0049-z

CRISPR/Cas9 Screening Using Unique Molecular Identifiers

B Schmierer, SK Botla, J Zhang, M Turunen, T Kivioja, J Taipale. Mol Syst Biol 13 (10), 945 2017 Oct 9. PMID: 28993443 DOI: 10.15252/msb.20177834