Wet lab

Central national infrastructure for high-density data

1. Laboratories

Central Next Generation Sequencing laboratory

In establishment. The laboratory will offer ELIXIR-SI owned state of the art NGS and other high-throughput laboratory equipment, tools and services.

Laboratory for single cell analysis

In establishment. The laboratory will offer ELIXIR-SI owned state of the art equipment, tools and services for single cell analysis, including 10x Genomics Spatial, Gridion Nanopore and Inverted Confocal Microscope.

Other laboratories

2. Research equipment

ELIXIR-SI RI-SI-2 project Research equipment

Central Next Generation Sequencing laboratory

The nCounter® SPRINT Profiler (manufactured by NanoString Technologies, Inc.) allows simultaneous quantitative analysis of up to 800 nucleic acid sequences (DNA and RNA) or proteins in a sample (or simultaneous quantitative analysis of up to 200 nucleic acid sequences in 4 samples). Fluorescently labeled probes bind to specific nucleic acid sequences in the sample, while unbound probes are removed during sample preparation.

 

 

Using a microscope and computer image analysis, the system determines the type and number of bound probes and thus enables the quantitative analysis of nucleic acids and proteins. The advantage of the system is the quick and easy preparation of the sample for analysis, while no amplification, transcription into cDNA and library preparation is needed. It also allows analysis of complex samples such as FFPE (Formalin-Fixed Paraffin-Embedded) samples, tissue samples, lysates and fluids.

 

Location: ELIXIR-SILVR (KRVS) unit.

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

The SeqStudio Genetic Analyzer is the fourth generation of 4 capillary, electrophoresis (CE) so-called Sanger sequencers. SeqStudio is an automated capillary electrophoresis system for nucleic acid analysis. It automatically performs sampling, polymer exchange, DNA separation and simultaneous detection of fluorescence in 4 capillaries. The system supports both sequential and fragment analysis on a plate (96-well) or in tubes (8-set) at the same time. Additionally, it allows the addition of new samples during the analysis. The work analysis program can be prepared on a computer, on the device itself (large touch screen), downloaded via WI-FI, LAN communication.

 

SeqStudio supports the same reagents as other Applied Biosystems multi-capillary sequencers (family 3500 and 3730, old systems 310 and 3130). Chemistry of BigDye ™ Terminator 1.1 Kit and BigDye ™ Terminator 3.1 Kit terminator are used for sequence analysis. Several dye chemistry is supported to perform fragment analysis, up to and including the last six dye chemistry.

 

The main applications are: plasmid sequencing, analysis in oncology (mutation confirmation-orthogonal technology), species identification, CRISPAR-Cas9 analysis – genome editing (diagnostics, pharmacy), forensic analysis, SNP analysis (SNAP shot genotyping), multiplex ligation ( MLPA; CNV) and other analyzes in pharmacy, diagnostics, environmental protection, microbiology.

 

In addition to classical sequential and fragment analyzes, the system enables various analyzes useful in diagnostics from HLA, CF, HIV, analysis of bacterial and fungal communities, comparative sequencing, validation of certain regions.

 

Location: ELIXIR-SILVR (KRVS) unit.

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

Quant Studio 7 Pro is a modular system of the latest generation of Real-Time PCR instruments from Applied Biosystems (part of Thermo Fisher Scientific).

 

The Real-Time PCR module allows the use of fast 96- and 384-well thermal blocks to perform a Real-Time polymerase chain reaction (quantitative PCR) and to perform some functions via voice commands. It allows the rapid and accurate identification of single nucleotide (SNP) polymorphisms in the studied sample by the HRM

function. The optics allows the differentiation of 21 different fluorescent dyes in the excitation range of 450-600 nm and in the detection range of 500-640 nm.

 

The digital module Studio 3D enables quantitative PCR applications without the use of a reference or standard curve with the possibility of use in many areas. The PCR amplification reaction takes place on a semiconductor chip with a capacity of 20,000 wells.

 

All necessary software for data acquisition and processing is included.

 

Location: ELIXIR-SILVR (KRVS) unit.

QuantStudio 7 Pro Real-Time PCR system
QuantStudio™ 3D Digital PCR Instrument

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

The upright confocal laser scanning microscope is equipped with a motorized microscope table which enables scanning along the x and y axes and focusing along the z axis.

 

It contains 10x, 40x and 63x objectives, 448 nm, 488 nm, 552 nm and 638 nm wavelength lasers and two scanning detectors, one of which is a super sensitive GaAsP detector. To ensure optimal conditions for multicolor imaging, the detectors provide a freely adjustable wavelength detection bandwidth.

 

The software allows time-lapse imaging in xyz coordinates, uncoupling the spectra of individual fluorescent dyes and motorized scanning of multiple regions of interest. The main advantage of the microscope is the large working distance (25 cm) between the motorized microscope table and the target focal plane, which allows in-vivo observation of large samples, such as plants.

 

Location: ELIXIR-SILVR (KRVS) unit.

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

Laboratory for single cell analysis

The LSM 900 confocal microscope allows the study of the three-dimensional distribution of fluorescently labeled molecules in cells and tissues. It is adapted to work with in vitro systems such as cell and tissue cultures, organoids and tissue slices.

 

 

The confocal system includes a chamber for maintaining cells at an adjustable temperature and gas concentration (CO2 and O2), which allows long-term experiments on living cells and the study of cell-physiological processes in these cells.

 

 

Location: UL MF (KRZS).

 

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

 

 

The Chromium Controller enables Chromium Single Cell (SC) and Linked-Reads Genomics Solutions. Chromium SC analyses include gene expression, epigenetics (ATAC), cell surface proteins analysis, immune profiling and targeted gene expression on a single-cell level.

 

The Chromium platform, powered by Next GEM technology, enables integrated analysis of SC at a massive scale. The key to this technology is the ability to generate tens of thousands of single-cell partitions, each containing a unique identifying barcode for downstream analysis.

 

Location: UL MF (KRZS)

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

 

GridION is a third-generation sequencer from Oxford Nanopore Technologies, which enables long DNA, RNA or cDNA fragments sequencing. Nucleic acid sequence identification is based on the change in electric current during the passage of DNA/RNA through a protein pore.

 

Sequencing can take place on 5 flow cells simultaneously, on which up to 150Gb can be read in total, thus enabling the sequencing of genomes and transcripts of all types of organisms, including humans. Nanopore technology enables sequencing and assembly of as yet unknown genomes. The computer capacity of GridION enables base-calling in real time and thus enables monitoring and control of the sequencing process.

 

Location: UL MF (KRZS).

 

Equipment reservation

In case the desired date is not available, please write to us at info@elixir-slovenia.org

Other laboratories
UM

Preparative flash/HPLC chromatograph puriFlash® 5.250 is used for the isolation of pure compounds from complex mixtures, e.g. natural extracts. It enables isocratic, as well as gradient (up to 4 solvents) separations that are performed either at low pressures (flash chromatography) or high pressures (up to 250 bar – preparative HPLC). The presence of compounds in the eluent is detected by DAD and ELSD detector. Because the system is equipped with an autosampler and fraction collector, work with it is highly automated.

 

 

The instrument, among other possible usages, enables isolation of pure compounds from natural extracts and therefore enables studies, which would elucidate connections between the structure and function of natural compounds. The experimental results, obtained on pure compounds, will also be explained by methods of computational chemistry.

 

 

Till now, the method for isolation of xanthohumol from hop extract was developed, while the isolation of sufficient quantity for testing the antibacterial activity is in progress.

 

 

Location: UM, FKKT (KRVS)

Other research equipment

KI
  • Cryo-transmission electron microscope with basic IKT support
  • ARC High performance computing center
KIS
  • Hyperspectral cameras:
    • The two pushbroom imaging spectrometers; HySpex VNIR (spectral range 400–988 nm) and SWIR (950–2500 nm) (Norsk Elektro Optikk AS),
    • Multispectral camera 5 bands, RedEdge (Micasense)
NIB
  • Several qPCR machines (Thermofisher, Roche) and Hamilton pipetting robot
  • Droplet digital PCRs QX100 (BioRad)
  • Chamber digital PCR BioMark HD (Fluidigm)
UKCLJ

CISLD

  • NGS sequencers (Illumina Miseq, ONT MinION)
  • NGS library prep infrastructure (enrichment, WGS, RNASEQ, ChIPSeq, long-reads libraries, miRNA-SEQ, Epi-SEQ)
  • cfDNA/RNA infrastructure
  • Cell Lab
  • Brightfield and Flourescent Microscopy Infrastructure
KIMG
UL BF
  • NGS sequencing machine IonProton™ including all necessary equipment
  • Sanger sequencing machine ABI Prism 3130XL with 16 capillaries
  • Equipment for DNA/RNA/protein analysis (PCR, qPCR, electrophoresis, gel documentation system, samples quantification)
  • Linux server with 12 cores, 170 GB RAM, 18 TB disk space
  • Software: CLC Genomics Workbench, CLC Genomics Server, Codon Code Aligner, BLAST2GO command line
UL MF

CFGBC

UL VF
  • Ion Torrent PGM sequencer with Ion OneTouch2 (Ion Torrent, Thermo Fischer Scientific)
  • Ultrasonicator Covaris M220 Focused
  • 1 x system for the evaluation of DNA, RNA and proteins LabChip GX (Caliper – Perkin Elmer)
  • Dell PowerEdge R730 Server
  • MALDI-TOF mass spectrometer (Bruker Daltonics Inc.)
  • 2 x real time PCR instrument ABI PRISM 7500 Real Time PCR System (Applied Biosystems)
  • 1 x real time PCR instrument Rotor-Gene Q (Qiagen)
  • 2 x real time PCR instrument (LightCycler 1.2, 2.0 LightCycler, Roche)
  • 1x realtime PCR instrument QuantStudio 5 Real-Time PCR Systems (Applied Biosystems)
  • 1 x digital PCR 3D QS (Applied Biosystems)
  • capillary sequencer (ABIPRISM 310, Applied Biosystems)
  • Several PCR instrument (Biometra, AB-Thermo Fisher)
  • 1 x system for gel documentation GenGenious (Syngen)
  • 1 x capillary electrophoresis QIAXCEL (QIAGEN)
  • Ultracentrifuge cooling (Beckman)
  • 1x Kingfisher automated nucleic acid extraction instrument
UM
  • Computer cluster KROP1
  • Computer cluster KROP2
  • 2x UV/Vis spectrophotometer
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