Stem cells & Genome editing
Platform services
Cell and reporter lines distribution
Generation of knockout human iPS cell lines
Derivation of characterization of human iPS cell lines
Neuronal differentiation of human iPS cell lines
Generation of brain organoids
Continuous visualization of live cells
Training
Cell line editing
Pooled CRISPR screening
Analytic genome editing services
Distribution of guide RNA clones from arrayed genome wide human and mouse CRISPR/Cas9 libraries
Flow cytometry to analyze and isolate edited cells
Mouse bone marrow/stem cell isolation followed by CRISPR editing
Contacts
Stem cell research is one of the most rapidly developing areas in biomedicine. The combination of genome editing with patient derived induced pluripotent stem cells (iPS cells) provides endless possibilities for cellular modelling of disease mechanisms and a platform for drug discovery. While the generation of human iPS cell lines has become a routine technology, it still requires special expertise, experience, and facilities. At the same time, know-how and technology development for differentiating cells to true models of human cells and tissues is becoming a bottleneck for taking full advantage of human iPS cell methodology. This is especially true for brain diseases, which form the largest societal burden of human diseases, and brain is the tissue composed of the most numerous cell types in the human body. These approaches can be effectively applied to study monogenic diseases using cell types that are otherwise not available for research. Furthermore, the approach is not limited to monogenic diseases but can also be used to study the functional effects of disease-associated genetic variants and the influence of environmental factors in defined cellular systems.
Genome editing toolbox is one of the most rapidly expanding set of ubiquitous research tools for life sciences based on CRISPR genome editing technology that was awarded Nobel prize in chemistry in 2020. Stem cells and genome editing platform aims to maintain and systematically build resources and services for in vitro and in vivo genome editing purposes as well as to maintain physical facilities enabling wide use of the resources across the Finnish biocenters. FinGEEC will provide facility services, general services and develop beyond-the-state-of-art genome editing technologies with partners from Helsinki, Turku and Kuopio.
Cell and reporter lines distribution
BF network offers a large range of human embryonic (hESCs), induced pluripotent stem cell (iPS cell) and iPS cell reporter lines with a complete service package including protocols for the stem cell maintenance and expansion, characterization data documentation and highly qualified technical support. BF network can assist with the selection of the appropriate stem cell line for your specific research needs.
Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
BioMediTech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center
Generation of knockout human iPS cell line
We offer the generation of knockout human PS cell lines using CRISPR/Cas9 technology. Genetically modified iPS cell lines can be developed according to customer's needs.
Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
Derivation and characterization of human iPS cell lines
BF network offers custom iPS cell line production service. Currently the methods for iPS cell generation are based on non-integrative technologies (Sendai virus, episomal vector and CRISPR activator) for reprogramming of somatic cells transduction. Reprogramming method is selected according to customer’s needs.
Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
Biomeditech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center
Neuronal differentiation of human iPSC lines
Human iPSC lines are differentiated into various types of neurons, including mixed and specific cortical neurons, dopaminergic neurons, motoneurons, astrocytes, microglia, and brain vascular cells including brain endothelial cells and pericytes. These services can be tailored according to customers’ needs, and the cell products can be delivered to customers or also analyzed as a service. The service can also include transplantation of these differentiated cells into immunodeficient mice for further analysis in vivo.
Helsinki Institute of Life Science - HiLIFE
Neuronal iPSC core in Neuroscience Center
Generation of brain organoids
Human iPSC lines are grown to brain organoids with or without including brain immune cells (microglia) or brain endothelial cells. The services includes an option for organoid transplantation into immune deficient mice.
Helsinki Institute of Life Science - HiLIFE
Neuronal iPSC core in Neuroscience Center
Continuous visualization of live cells
The IncuCyte S3 automatically acquires and analyzes images around the clock, providing an information-rich analysis. IncuCyte S3 accommodates up to six microplates at a time. Users can schedule experiments at different image acquisition frequencies and magnifications in parallel. Remote, networked access with unlimited, free licenses.
Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
BioCity
FinGEEC-Turku
Training
BF network offers hands on laboratory-based training in fundamental aspects of pluripotent stem cell culture and analysis.
- Training packages tailored for the client's needs in stem cell culture.
Helsinki Institute of Life Science - HiLIFE
Biomedicum Stem Cell Center
Biomeditech, Tampere University
iPS Cells
Biocenter Kuopio
Stem Cell Center
Cell line editing
The service enables generation of disease relevant cellular model systems including knock-outs, knock-ins, and either creation or reversion of pathogenic mutations. This service also facilitates generation of reporter cell lines with fluorescent or other kinds of tags. Cellular systems can be created to facilitate genetic screening and drug screening. Furthermore, cell line editing can be used to validate hits from genetic screens or drug screens. Much needed isogenic cell lines for isogenic disease models can be generated by cell line editing.
Target cell type and intended type of editing will determine the approach and feasibility of editing projects. The projects are initiated together with scientists requiring the services. Therefore, there will be evaluation phase when FinGEEC personnel will determine whether the project is currently doable and whether the client agrees with the price and duration of the project, and risks involved.
Note that this service is not currently provided for primary cells. For human pluripotent stem cell editing, please, contact BSCC, HiLIFE, UH.
Helsinki Institute of Life Science - HiLIFE
FinGEEC-Helsinki
Biomeditech, Tampere University
iPS Cells
BioCity
FinGEEC-Turku
Pooled CRISPR screening
Pooled CRISPR screening is extremely versatile method. Practically any phenotype that allows cell separation can be queried. Essential genes in specific cell types can be determined by pooled CRISPR screening or drug resistance and sensitivity genes can be discovered. Novel genes and pathways involved in cell differentiation can be mapped. These screens can be performed in cell lines, stem cells (BSCC, HiLIFE, UH) or primary cells, however, we currently have the service setup for established cell lines only.
Pooled CRISPR screens provided by FinGEEC-Turku are highly customized and are designed, and performed in collaboration with clients. Pooled CRISPR screens currently mostly rely on lentiviral gene transfer, therefore, this service is closely coordinated together with local VGTCT nodes
Please, see Addgene plasmid repository has most of the genome-scale pooled CRISPR libraries readily available as DNA preparations for a price as low as 500 dollars per library.
BioCity
FinGEEC-Turku
Analytic genome editing services
Analytic gene editing services include 1) SURVEYOR analysis for editing efficacy, 2) Edited sequence analysis by Sanger seq, 3) TOPO TA clone analysis to identify exact editing events.
Helsinki Institute of Life Science - HiLIFE
FinGEEC-Helsinki
Distribution of guide RNA clones from arrayed genome-wide human and mouse CRISPR/Cas9 libraries
FinGEEC-Helsinki holds unique national resource of human and mouse arrayed genome-wide lentiviral CRISPR/Cas9 sgRNA libraries from Merck/Sigma-Aldrich (designed by Welcome-Trust Sanger Institute) (Winner of 2016 R&D 100 prize, Metzakopian, PMID: 28533524) in bacterial glycerol stock format. FinGEEC-Helsinki is responsible for distributing clones from these libraries as glycerol stocks or as DNA preparations for BF-based customers. This service provided in collaboration between FinGEEC-Helsinki and Genome Biology Unit (GBU) (HiLIFE and part of Genome-wide methods of BF). Cas9 enzyme is not included in these constructs. We advise clients to see Addgene resources for different Cas9 expression vectors or commercial sources for Cas9 expression in various formats.
Helsinki Institute of Life Science - HiLIFE
FinGEEC-Helsinki
Flow cytometry to analyze and isolate edited cells
FinGEEC-Kuopio provides facilities and equipment for flow cytometric sorting and analysis of cells generated with viral vectors and novel genome editing technologies. Cell preparations can be either cell lines or cells isolated from tissues. The services are based on the following instruments and full hands-off service:
- FACS Aria III sorter (Becton Dickinson) equipped with three lasers
- A-state-of-the-art imaging cytometer, FlowSight (Merck Millipore) with 4 lasers
- A new analyzer CytoFLEX S with 4 lasers (Beckman-Coulter)
Biocenter Kuopio
FinGEEC-Kuopio
Mouse bone marrow/ stem cell isolation followed by CRISPR editing
This service is based on published method where mouse stem/ progenitor cells are modified using lentiviral vector approach (Mäkinen et al. Cardiovascular Research, 2010, 88:530-538). Optionally, these cells can be further used for reconstitution of adult mouse bone marrow.
Biocenter Kuopio
FinGEEC-Kuopio
Contact persons
Platform Chair
Timo Otonkoski / timo.otonkoski (at) helsinki.fi / tel: +358 2941 25692
University of Helsinki, HiLIFE
Biomedicum Stem Cell Center
Platform Vice Chair
Topi Tervonen / topi.tervonen (at) helsinki.fi / tel: +358 2941 25494
University of Helsinki, HiLIFE
Finnish Genome Editing Center- Helsinki (FinGEEC-Helsinki)
Platform partners
Timo Otonkoski, Biomedicum Stem Cell Center (BSCC), HiLIFE, UH (chair of the consortium); Katriina Aalto-Setälä, iPSC Cells, BMT, UTA; Riikka Martikainen, Stem Cell Center, Biocenter Kuopio, UEF; Jari Koistinaho, BSCC, HiLIFE, UH; Topi Tervonen, Finnish Genome Editing Center (FinGEEC)-Helsinki, HiLIFE, UH (vice chair); Johanna Ivaska, FinGEEC-Turku, Biocity, UTU; Petri Mäkinen, FinGEEC-Kuopio, Biocenter Kuopio, UEF