The Biomedicum Helsinki building houses several units that provide centralized services to the investigators, i.e., core facility services. These core facility services are available for all research groups working on the Meilahti medical campus. In addition, private institutions, research groups and companies located outside the Meilahti campus are permitted to use the services or buy the products of the core facilities. The prices of the services or products are dependent on the organization of the user or buyer.
CORE FACILITY SERVICES
The facility has its own computing cluster and enterprise class storage area network (SAN) storage system. The unit is connected to the University of Helsinki network, and it is separated behind its own firewall. In addition to establishing the computing environment, the unit also provides expert help in bioinformatics and biocomputing to research groups and individual investigators.
The principal services include, but are not limited to, the following:
- sequence analyses - from short oligonucleotide and peptide sequences up to genome-wide sequences
- storage of data resources, analyses of large data sets pertaining to sequencing, gene expression profiling and genotype analyses, and integration of multiple data sets
- linkage and association analysis of genotyping data sets
The hardware, software and personnel of the unit provide collectively an interactive environment to analyze large data sets in a multifaceted manner.
Timo Miettinen, timo.a.miettinen (at) helsinki.fi
FIMM-HCA provides access and assistance in high-content microscopy and data analysis. Our high-content screening systems are available as a service and for independent users. We provide assistance for the whole process from imaging to data analysis.
Lassi Paavolainen, lassi.paavolainen (at) helsinki.fi
Biomedicum Functional Genomics Unit (FuGU) provides a wide range of services related to functional genomics. These services cover areas such as genome profiling (microarrays and next-generation sequencing), computational analyses and virus mediated gene silencing and overexpression. FuGU also houses a genome-wide shRNA library that contains hairpins for 16,000 human and mouse genes each. These hairpins are available for researchers as glycerol stocks, DNA or lentiviral particles. The unit operates under the national Biocenter Finland infrastructure network.
Outi Monni (Director), e-mail: outi.monni (at) helsinki.fi
Juha Klefström (Scientific director), e-mail: juha.klefstrom (at) helsinki.fi
Biomedicum Stem Cell Center (BSCC)
BSCC is a research unit and collaborative facility at the Biomedicum Helsinki. It focuses on human embryonic stem cells (hESC). BSCC distributes the locally derived hESC lines to other researchers and offers technical help and training in the culturing and genetic modification of hESC.
Prof. Timo Otonkoski, e-mail: timo.otonkoski (at) helsinki.fi
Docent Timo Tuuri, e-mail: timo.tuuri (at) helsinki.fi
Tea Vallenius, bch-gbu (at) helsinki.fi
Kaisa Laajanen, bch-gbu (at) helsinki.fi
FIMM Sample Storage Service offers reliable low cost sample storage in liquid nitrogen vapour phase (-180°C) or at RT. For this purpose, FIMM has dedicated professional staff, detailed operations and modern appropriate sample storage systems and LIMS. Sample storage service unit offers also assistance in ethical aspects and legislative issues on biobanking for writing applications e.g. for ethics committee in terms of sample collecting.
Currently we are storing human blood, serum, plasma, bone marrow, and urine samples. Our main polices are that collaboration is based on a written agreement and that there will be no change in the ownership of the samples unless otherwise agreed.
Tiina Vesterinen, e-mail: tiina.vesterinen (at) fimm.fi
The University of Helsinki EV core is a co-operational venture of the Department of Biosciences and the Faculty of Pharmacy (Viikki campus) and the Institute for Molecular Medicine Finland (FIMM) consisting of two laboratories dedicated to extracellular vesicle (EV) research. As an academic research and service facility, the EV core provides infrastructure, state-of-the-art and emerging EV-technologies for research groups, hospitals, companies and authorities in the EV-field. The EV core facility provides diverse EV isolation, purification and characterization services and can offer contacts to various downstream analyses in other core facilities based on optimized EV-protocols.
The EV-research group in Viikki focuses on understanding how EV-signals from varying cellular sources mediate and regulate cell behavior and cross-talk e.g. during development, in immunity and inflammation, and how EVs could be utilized in diagnostics and therapeutics. EV-research at FIMM focuses on liquid biopsy disease biomarkers taking advantage of the national sample collections, for example in the Helsinki Urological Biobank. Together, the EV core members have further developed the EV-know-how in a research consortia mixing academia and companies managed by the SalWe Ltd.
The expertise of the EV core encompasses:
- Sample handling and storage
- Sample material requirements (plasma, urine and cell culture media etc.)
- EV isolation with traditional and new methods
- Low-amount analysis methods: particle, protein, nucleic acid, lipid, protein, metabolomics and EM analysis (partially through collaboration with other core facilities within the University of Helsinki)
- EV-specific data analysis/normalization
Head of the EV core Viikki, Docent Pia Siljander, pia.siljander m(at)helsinki.fi, tel +358 (0) 504486373, +358 (0) 294159023
Coordinator Viikki, Mari Palviainen, PhD, mari.palviainen (at) helsinki.fi, tel +358 (0)5 0 4480777, +358 (0) 294159307
Head of the EV core FIMM, Maija Puhka, PhD, maija.puhka (at) helsinki.fi, tel +358 (0) 400 826846, +358 (0) 2941 25879
ev-core (at) helsinki.fi
FIMM Digital Microscopy and Molecular Pathology Unit
Core summary: Digital microscopy and molecular pathology unit provides high throughput whole-slide scanning services for all customers. We offer quick, high-quality and cost-efficient wide-field microscope imaging for bright field and fluorescence. We can provide your digitized slide data with WebMicroscope software. The webmicroscopy is developed by the Lundin group at FIMM. It is a method of digitizing entire microscope specimens and viewing as well as processing the virtual slides through a web interface. More information: http://www.fimmic.com/ . FIMM also provides know-how on automated assessment of cell and tissue sample with image analysis.
Reija Randen-Brady, e-mail: Reija.Randen-Brady (at) fimm.fi
Tapio Tainola, e-mail: tapio.tainola (at Helsinki.fi
The Molecular Medicine Sequencing Laboratory provides low-cost, high quality sequencing and fragment analysis services for Biomedicum researchers using an ABI2720 96-capillary instrument. In year 2005 Sequencing laboratory produced over 158 000 sequences (>60 Mb) for its customers.
The services include:
- FullService sequencing: incl. sequencing reaction, purification, electrophoresis run and storing of the results into database
- Ready-to-Run sequencing: incl. purification, electrophoresis run and storing of the results into database
- FragmentAnalysis run: incl. electrophoresis run and storing of the results into database
Pekka Ellonen, e-mail: pekka.ellonen (at) fimm.fi or pekka.ellonen (at) helsinki.fi
Sequencing Core Facility (Haartman-Institute)
Sequencing Core facility serves all customers by sequencing customer templates (PCR -fragments, clones) using Applied Biosystems Dye Terminator (v.3.1) sequencing kit and reactions run on 3100 capillary sequence analyzer. Unit provides commercial primers (M13 Forw and Rev, T7, T3, SP) for sequencing.
Paula Kristo, e-mail: paula.kristo (at) helsinki.fi
Large scale DNA extraction and storage facility
The facility presently houses DNA from more than 200 000 individuals and is co-ordinated by National Public Health Institute. It is equipped with state of the art bar coding system for sample tracking, an automated Gentra DNA extraction equipment, liquid handling robots, storage facilities, and tailor made data management tools for optimal confidentiality and quality control.
The services of the facility include:
- DNA extraction: blood, solid tissue, cells, buccal swab
- DNA dilution and aliquoting
Dr. Päivi Laiho, e-mail: paivi.laiho (at) thl.fi
The service offers flexible liquid handling and detection instrumentation for versatile screening assays or just for automation of vast and laborious molecular biological methods (example pipetting of 20000 PCR reactions). The facility has small molecule library to offer to the customers that could be used for example in screening antagonists or agonists for certain G-Protein Coupled Receptor or screening of inhibitors for certain protein-protein interaction. In addition, RNAi-library is under development for genetic screening assays. The service supports the customer in developing their assay and helps in assay automation. Prenegotiated material prices are also available for customer convenience.
Maxim Bespalov, e-mail: maxim.bespalov (at) fimm.fi
Animal Facility and Transgenic Unit
The unit aims at being a modern transgenic animal facility that furnishes the users with multiple services. The services include injection of gene constructs to fertilized oocyte nuclei to produce transgenic animals and production of knockout animals by using embryonal stem cells. In addition, the unit carries out embryo transfer and embryo freezing. The user of the services needs to prepare gene constructs and produce gene-targeted embryonal stem cells. The facility will collect tissue samples from animals for genotyping, and it will take care of animal breeding according to the instructions of the user.
The transgenic animal facility is a part of the Experimental Animal Center of the University of Helsinki at Meilahti Campus.
The rodent phenotyping and in vivo experimentation unit (Rofe) offers services and training for research related to various disease models and rodent phenotyping. Rofe offers services for research related to rodent (mouse, rat) disease models of psychiatric disorders, integrative neurophysiology, cardiovascular and metabolic testing. In addition, Rofe has equipment and methodology for analysis of locomotor activity and motor coordination as well as sensory, emotional and cognitive functions.
Contact: Anni-Maija Linden, rofe-manager at helsinki.fi
Esko Kankuri, e-mail: esko.kankuri (at) helsinki.fi
The service includes cryosectioning, immuno-histochemical staining, and in-situ hybridization, in addition to paraffin sectioning and histological staining services.
e-mail: tissue-service (at) helsinki.fi
The unit has at its disposal the requisite equipment needed in modern microchemical protein analyses as well as protein purification and isolation. Special services include identification and sequencing of proteins, characterization of protein interactions and proteome analysis of samples.
The services furnished by the unit also include supervised working in its premises and regular training courses in modern protein chemistry organized by the unit personnel.
Director of the unit:
Dr. Marc Baumann, e-mail: marc.bauman (at) helsinki.fi
The personnel responsible for the services include a researcher and a research technician.
Peptide and Protein Laboratory (Haartman-Institute)
Hilkka Lankinen, e-mail: hilkka.lankinen (at) helsinki.fi
The services of the unit cover large-scale production of cells - primarily eukaryotic cells - and proteins produced by the cells. The facility is located in specially designed laboratory environment and is equipped with a modern 50-liter bioreactor together with accessory instrumentation. Insect cells and baculovirus vectors are mainly used for production of proteins. Initial preparative protein purification can be provided as the service of the unit, but the final down-stream processing is the responsibility of the research group using the facility.
The unit is a cooperative project by the University of Helsinki and Helsinki University of Technology.
Biomedicum Imaging Unit (BIU) provides equipment, training and consultation services for advanced functional and molecular imaging of cells, tissues and organisms, as well as data processing and analyses. Our resources are located at the Biomedicum 1 building and Haartman Institute.
The equipment include several live-cell confocal, widefield and TIRF microscope workstations, optical and fMRI whole animal imaging systems, a cell-based high content screening system, inverted and upright epifluorescence microscopes, and high-end software for deconvolution, volume reconstruction and image analysis. We provide our users with state-of-the-art equipment, tailored training and continuous support, and research project consultation. BIU organizes regular workshops, seminars, and practical and lecture courses, and fosters contacts with national and international partners in bioimaging.
Our services are open for all students, researchers and commercial customers irrespective of their locations and affiliations. Please see further details and oncoming events on our web-pages.
biu-support (at) helsinki.fi and http://www.biu.helsinki.fi/
Functional MRI Unit
The 4.7 tesla fMRI equipment of the unit permits fast and accurate imaging of rodent (mouse, rat) organ structure and organ function. In addition to the imaging instrumentation, the unit has special facilities for surgery and handling of small experimental animals.
The unit of a collaborative project by Helsinki University Central Hospital and University of Helsinki.
Director of the unit:
Turgut Tatlisumak, e-mail: turgut.tatlisumak (at) hus.fi
Biomedicum FACS Core Facility provides flow cytometric analysis and cell sorting services as well as flow cytometry training and education for new users. Flow cytometry is a method that allows measurements of various characteristics of individual cells by using fluorescent probes.
Nina Peitsaro, e-mail: nina.peitsaro (at) helsinki.fi
Noora Aarnio, e-mail: noora.m.aarnio (at) helsinki.fi
Tarja Grundström, e-mail: tarja.grundstrom (at) helsinki.fi
Manager of the unit:
Juha Klefström, e-mail: juha.klefstrom (at) helsinki.fi
Michael Jeltsch, e-mail: michael (at) jeltsch.org
Marko Hyytiäinen, e-mail: marko.hyytiainen (at) helsinki.fi
Andrey Anisimov, e-mail: andrey.anisimov (at) helsinki.fi
Tanja Laakkonen, e-mail: tanja.laakkonen (at) helsinki.fi
HUSLAB Media Production Unit
liuoslaboratorio (at) hus.fi
The unit is responsible for production of culture media and buffer solution, including:
- culture media for bacteria, yeast and animal cells
- sterile buffer stock solutions
- sterile water
- various other sterile solutions as specified by the user
At present, the unit produces over 100 different media and solutions.
Kirsti Iivonen, e-mail: kirsti.iivonen (at) hus.fi
Senior Advisors support researchers in preparation of research funding proposals, contract negotiation and issues related to management and administration of the projects, organize training and provide information on funding possibilities.
The services are focused on the preparation and contract negotiation phases of the application process.
University of Helsinki
Research Funding Services
Biomedicum Helsinki, A408b
P.O. Box 63 (Haartmaninkatu 8)
00014 University of Helsinki, Finland
Phone +358 02941 25129
GSM +358-50-442 2450
Research Sector: http://www.helsinki.fi/tutkimuksen-toimiala/index_eng.html
Helsinki Innovation Services (HIS Ltd): http://www.his.fi/en/
Clinical Research Unit
The unit encompasses a special office and research space - a total of 150 m2 - where the user can interview, examine and monitor volunteered study subjects as well as take blood and tissue samples.
The space, or a part of it, can be rented for a defined time period.
HUCH Institute Ltd.