The ERA Chair’s laboratories are state of the art facilities that encompass a range of different technologies important for life science research. These facilities are located on three floors of the SIME building and in the department of Pathophysiology on the 4th floor of Biomedicum both in Tartu.
These facilities are:
CELL CULTURE FACILITIES
State of the art cell culture facilities allow different cell culture technologies both at the 2-Dimensional and 3-Dimensional level. These facilities allow primary cell cultures as well as a range of immortalised cell lines from Human and different species. Cell culture facilities in conjunction with cell verification and freezing storage facilities ensure constant supply of cells for different phenotypic, genomic and transcriptomic analysis.
HIGH THROUGHPUT GENOMIC FACILITIES
We have cutting edge equipment for high throughput genomic analysis. These include the following:
Ion Torrent System
We have different Ion Torrent platforms – one Ion Torrent PGM (Personal Genome Machine) and two Ion S5 XL instruments together with two Ion Chef platforms and all the other supportive equipment needed. Ion Torrent instruments are next generation sequencers, which detect changes in pH during sequencing and no camera or imaging is needed. Thus, the platforms are perfect for fast and easy sequencing. Ion PGM with a smaller throughput is ideal for targeted or microbial sequencing – three different-sized chips allow us to get 400 000 to 4 million reads with one run. Ion S5XL is with a high throughput and applicable for whole exome and transcriptome studies – three different chips provide 3 million to 80 million reads per run. The length of the reads can be up to 400 base pairs. Within two days sequencing starting from library preparation and data analysis could be performed. Additionally, Ion Torrent System has several ready to use panels suitable for both RNA and DNA sequencing (Ion AmpliSeq Target Selection Technology).
Affymetrix Gene Chip Arrays
The facility offers services on the Affymetrix GeneTitan Instrument and the affymetrix microarray platforms. The device combines hybridization, fluidics, and scanning and basic data analysis in a single unit. The instrument is suitable for high throughput genotyping projects, which will be carried out on 96-format array plates, and the system possesses two plates per day and up to 750 samples per week. GeneTitan Instrument also supports gene expression analyses on 16-, and 24-format array plates.
Real-time PCR Technology
Fast Real-Time PCR System suitable for smaller projects and is applicable for both genotyping and gene expression studies. TaqMan SNP genotyping assays provide a detection of polymorphisms within any genome. Workflow is based on 5’ nuclease assay chemistry with TaqMan MGB probes. Assays are ideal for genotyping applications including screening, association, candidate region, candidate gene, and fine-mapping studies.
DATABASES AND BIOINFORMATIC ANALYSIS FACILITIES
We store the raw data produced by either sequencing or microarray-based technologies in our own servers or in the servers of the manage sample and patient data we develop and maintain databases via the REDCap database client hosted by HPC . These databases presently contain more than 2400 entries from projects ranging from skin related research to bone tumours and joint replacement studies.
We perform several data analysis for sequencing and microarray data and develop our own custom workflows. We use a wide range of acknowledged freeware including components of GATK pipeline, R statistical software packages and commercial software like LifescopeTM Genomic Analysis Software, Torrent SuitTM Software, GraphPad Prism and CLC Genomics Workbench.
Our computational resources include the servers of sequencing platforms and a stand-alone computer cluster with four compute nodes. For more resource-demanding computations we have full access to the resources of HPC.
Laboratory Animal center
Our laboratory is closely collaborating with Laboratory Animal centre (sime.ut.ee). Through this collaborative link, ERA chair team has direct access to the state of the art Human disease models in animals, Transgenic Mouse and Rat services, In vivo small animal high field magnetic resonance imaging and spectroscopy and in vivo fluorescence imaging facilities.