Institute of Molecular Genetics of the Czech Academy of Sciences
The new Visium CytAssist is a compact, benchtop instrument that enables the transfer of transcripts or transcriptomic probes from standard glass slides to Visium and Visium HD slides, enabling spatial profiling insights to be gained from even more samples. Compatible with hematoxylin and eosin (H&E)- or immunofluorescence (IF)-stained tissue sections, CytAssist allows pre-sectioned tissues to be used for the Visium workflow. You can further maximize your Visium experiments by screening tissue sections using standard histological techniques to find biologically significant sections and then precisely align those sections within the Visium or Visium HD slide Capture Area using CytAssist.
The 10x Genomics Xenium Analyzer is an advanced, automated, imaging-based platform for in situ spatial transcriptomics and protein analysis. It enables sub-cellular mapping of hundreds to thousands of RNA targets directly within intact formalin-fixed, paraffin-embedded (FFPE) or fresh-frozen tissue sections, allowing high-resolution visualization of gene expression in its native tissue context. The Xenium platform delivers high-plex in situ at subcellular resolution with nanometre precision and offers a complete solution, including comprehensive panel offerings, to achieve fast and robust single cell spatial insights.
Key Features and Capabilities
Subcellular Resolution: Provides high-resolution imaging (resolution in tens of nanometers) to locate individual RNA transcripts within cells.
Targeted Profiling: Enables high-plex, targeted analysis of RNA (and protein) panels. Predesigned panels are available for human and mouse, custom panels are available for any eukarytoic species. Panels include hundreds to thousands of gene targets.
Integrated Workflow: Combines imaging, fluidics, decoding, and on-board data analysis in one instrument.
High Throughput: Assays up to 4 cm2 of tissue sections.
Output Data: Produces 3D Z-stack images for morphological context and cell segmentation, along with CSV/parquet files for transcript location.
PromethION offers the same real-time, long-read, direct DNA and RNA sequencing using Oxford Nanopore technology as MinION Mk1B, at much larger scale enabling users to apply the technology to large projects. The PromethION 2 Solo is a small benchtop device designed to run up to two PromethION flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or individually. The current chemistry and software enables generation of up to 290 Gbases* of data from a single PromethION flow cell (*theoretical max output based on sequencing at 420 bps for 72 hours). Typical output is 80-100 Gbases.
The Illumina NextSeq 2000 is an advanced high-throughput DNA sequencing platform. Key features include rapid run times, compatibility with various sample types and sequencing chemistries. The 2 channel Illumina Sequencing-by-Synthesis Technology ensures high-quality reads of low error rate. It supports diverse applications, such as whole-genome sequencing, targeted sequencing, RNA-Seq, ChIP-Seq, methylation sequencing, single cell sequencing, and more. The system delivers 10-360 Gb of sequencing data, 100 M – 2.4 B reads per run, with a maximum read length of 2 * 300 bp.
The Oxford Nanopore MinION Mk1b is a portable USB-powered, real-time DNA/RNA sequencer with a flow cell featuring 512 channels each connected to 4 wells with nanopores. The theoretical maximum output of a single flow cell is 48GB over 72 hours (400 bases/second). The actual output depends on application. It directly sequences short to ultra-long reads (longest > 4Mb), can detect modified bases, and requires no PCR in sample preparation. The single-molecule accuracy with Kit 14 Chemistry is > Q20 (99%) for simplex reads, and ~Q30 (99.9%) for duplex reads.
Applications include
The instrument allows multiplexing of smaller samples.
The 10x Genomics Chromium Controller is a platform designed for single-cell genomics such as single-cell RNA sequencing (scRNA-seq), single-cell ATAC sequencing (scATAC-seq), and more. It utilizes microfluidics technology to encapsulate and barcode individual cells into nanoliter-sized droplets, allowing for parallel processing of thousands of cells simultaneously.
More information – www.10xgenomics.com.
Formulatrix Mantis is a system for the handling of small volumes of liquids and reaction mixtures suitable for, among other things, the preparation of sequencing libraries and PCR reactions. It allows transferring liquid volumes as low as 100 nl while maintaining very high transfer accuracy and very low dead volume.
Technical specifications
CFX Opus is the newest real-time PCR system in BioRad‘s robust CFX Family. The CFX Opus 96 Real-Time PCR System can analyze 96 wells and offers a number of new features:
Applications and Uses
The LightCycler® 480 Instrument is intended for performing rapid, accurate polymerase chain reaction (PCR) in combination with real-time, online detection, enabling Absolute or Relative Quantification of a target nucleic acid, as well as post-PCR analysis of the amplified nucleic acid by Melting Curve analysis. The LightCycler® 480 Instrument is a rapid, plate-based, thermal block cycler with integrated real-time, online detection capabilities. The instrument provides extraordinary well-to-well temperature homogeneity and inter-well, inter-cycle reproducibility. The special arrangement of optical components in the LightCycler® 480 Instrument ensures uniform collection of signals across the plate and makes analysis independent of the sample position on the plate.
The optical system of the LightCycler® 480 Instrument has a lower limit of detection of 0.1 nmol/l Fluorescein, which corresponds to 2 fmol or 1.2 x 109 Fluorescein Molecules in a 20 μl reaction.
The AbsQuant analysis module of the LightCycler® 480 Software automatically performs arithmetic background correction.
Specifications of the Detection Unit
Excitation
| Type | Xenon reflector lamp |
| Wattage | 100 W |
| Lifetime | 500 h |
Detector
| Type | Xenon reflector lamp |
| Resolution | 1024 × 1344 pixel |
| Integration time | 10 ms to 10 s |
| Integration time selection | Dynamic or manual |
| Sensitivity | < 0.2 nmol/l fluorescein, typically 0.1 nmol/l (20 μl reaction volume) |
| Reproducibility | CV ≤ 0.15% |
| Crosstalk well-to-well | < 0.2% optically < 0.02% with software correction |
Optical filter
| Bandpass | Band Width (BW) | |
| Excitation wavelengths (nm) | 450 nm 483 nm 523 nm 558 nm 615 nm | 30 nm 35 nm 20 nm 30 nm 30 nm |
| Emission wavelengths (nm) | 500 nm 533 nm 568 nm 610 nm 640 nm 670 nm | 20 nm 20 nm 20 nm 20 nm 20 nm 20 nm |
| Type of block | LightCycler® 480 Thermal Block Cycler Unit (96-/384-well) |
| Sample volume | 96-well thermal block 10 — 100 μl 384-well thermal block 5 — 20 μl |
| Consumables | LightCycler 480 SYBR Green I Master LightCycler® 480 Probes Master Universal ProbeLibrary set LightCycler 480 Multiwell Plate 384 LightCycler 480 Multiwell Plate 96 |
| Software | LightCycler® 480 Software |
| Location | room no. 1.01 |
| Phone | ext. 3148 |
| Document | EN manual |
| Training | not required |
| Booking | Calpendo |
The LightCycler® 480 Instrument is intended for performing rapid, accurate polymerase chain reaction (PCR) in combination with real-time, online detection, enabling Absolute or Relative Quantification of a target nucleic acid, as well as post-PCR analysis of the amplified nucleic acid by Melting Curve analysis. The LightCycler® 480 Instrument is a rapid, plate-based, thermal block cycler with integrated real-time, online detection capabilities. The instrument provides extraordinary well-to-well temperature homogeneity and inter-well, inter-cycle reproducibility. The special arrangement of optical components in the LightCycler® 480 Instrument ensures uniform collection of signals across the plate and makes analysis independent of the sample position on the plate.
The optical system of the LightCycler® 480 Instrument has a lower limit of detection of 0.1 nmol/l Fluorescein, which corresponds to 2 fmol or 1.2 x 109 Fluorescein Molecules in a 20 μl reaction.
The AbsQuant analysis module of the LightCycler® 480 Software automatically performs arithmetic background correction.
Specifications of the Detection Unit
Excitation
| Type | White power LED |
| Wattage | 10 W |
| Lifetime | > 10,000 h |
Detector
| Type | Monochrome CCD camera |
| Resolution | 1024 × 1344 pixel |
| Integration time | 10 ms to 10 s |
| Integration time selection | Dynamic or manual |
| Sensitivity | < 0.2 nmol/l fluorescein, typically 0.1 nmol/l (20 μl reaction volume) |
| Reproducibility | CV ≤ 0.15% |
| Crosstalk well-to-well | < 0.2% optically < 0.02% with software correction |
Optical filter
| Bandpass | Band Width (BW) | |
| Excitation wavelengths (nm) | 440 nm 465 nm 498 nm 533 nm 618 nm | 35 nm 25 nm 40 nm 25 nm 35 nm |
| Emission wavelengths (nm) | 488 nm 510 nm 580 nm 610 nm 640 nm 660 nm | 20 nm 20 nm 20 nm 20 nm 20 nm 95 nm (long pass) |
| Type of block | LightCycler® 480 Thermal Block Cycler Unit (96-/384-well) |
| Sample volume | 96-well thermal block 10 — 100 μl 384-well thermal block 5 — 20 μl |
| Consumables | LightCycler 480 SYBR Green I Master LightCycler® 480 Probes Master Universal ProbeLibrary set LightCycler 480 Multiwell Plate 384 LightCycler 480 Multiwell Plate 96 |
| Software | LightCycler® 480 Software |
| Location | room no. 1.01 |
| Phone | ext. 3148 |
| Document | EN manual |
| Training | not required |
| Booking | Calpendo |
The QX200 is a droplet digital PCR system designed for precise and absolute quantification of target DNA or RNA molecules. The digital PCR technology makes the instrument highly sensitive, allowing detection of rare events or low-abundance targets in the sample. QX200 supports a variety of nucleic acid detection chemistries, including EvaGreen and probe-based assays.
Possible applications of the Bio-Rad QX200
The QX200 Droplet Digital PCR System consists of two instruments, the QX200 Droplet Generator and the QX200 Droplet Reader.
| Booking | Calpendo |
The Leica DMi8 microscope is a modular inverted widefield fluorescence microscope with fully motorized stage and both monochromatic (Leica K5) and color (FLEXACAM C3) cameras. The DMi8 microscope has DAPI, FITC and RHOD filter sets for fluorescence.
| The contrast techniques available | Brightfield Integrated Modulation Contrast Phase Contrast |
| Objectives | 5x/0.12 10x/0.45 20x/0.40 40x/0.95 |
All the features are fully implemented in LAS X software.
The Bio-Rad TC20 automated cell counter is a device used for counting and analyzing mammalian cells in one simple step, in less than 30 secconds. Upon insertion of a counting slide, the TC20 cell counter rapidly provides a total cell count (with or without trypan blue staining) and assesses cell viability via trypan blue exclusion.
| Counting time, sec | 30 |
| Cell concentration range, cells/ml | 5 x 104–1 x 107 |
| Optimal cell concentration range, cells/ml | 1 x 105–5 x 106 |
| Cell diameter range, µm | 6–50 |
| Sample volume, µl | 10 |
| Data storage, counts | 100 |
| Data export | Via USB flash drive |
| Printer connectivity | Yes |
| Dilution calculator | Yes |
| Image of cells available | Yes |
EnVision multimode plate reader for spectrophotometric measurements of assays carried-out on microtiter plates. The instrument is equipped with a monochromator and filters.
| Supported technologies | Absorbance Fluorescence Fluorescence polarization (FP) Time-Resolved Fluorescence (TRF) Time-Resolved FRET (TR-FRET, HTRF) Luminescence |
| Fluorescence, absorbance | 96, 384 and 1536 well plates Monochromator / filters (higher sensitivity) |
| Filter/mirror configurations | FITC fluorescence (485/535 nm) FITC fluorescence polarization (480/535 nm) HTRF (Europium cryptate) (320/615/665 nm) Other filters: 340, 380, 405, 460, 510 nm |
| Luminescence: | 96 well plates |
| Booking | Calpendo |
The Amersham Typhoon Scanner IP is a versatile laser scanner that can be used for imaging of storage phosphor screens (filmless autoradiography). It is suitable for phosphor imaging (laser excitation wavelength LD635) of radioisotopes (3H, 14C, 32P, 35S) with dynamic range > 5 orders of magnitude with high resolution. Special phosphor screens and stages (20×25 cm for 3H and 32P radioisotopes) are available on request in the Laboratory of Biology of the Cytoskeleton (Dr. Vadym Sulimenko, room no. 3.13, phone ext. 2640). All phosphor screens must be erased using the Amersham Eraser after use.
| Location | room no. 1.01 |
| Booking | Calpendo – Typhoon |
New users have to be first trained by Dr. Vadym Sulimenko.
Thermo Fisher Scientific UV-Vis spectrophotometer, micro-volume pedestal technology for nucleic acids and proteins concentration measurements.
| Minimal sample volume | 0.5 μL |
| Detection range | 2 – 15,000 ng/μL |
| Wavelength range | 190 – 840 nm |
| Measurement time | < 5 seconds |
Qubit 2.0 fluorometer is designed to work with highly selective Qubit DNA, RNA, and protein assays forming the Qubit Fluorometric Quantitation Platform, analyte-specific for proteins and nucleid acids with unprecedented accuracy, sensitivity, and simplicity.
| Minimal sample volume | 1 μL |
| Protein quantitation range | 250–5,000 ng RNA 4-20,000 ng DNA 0.1 – 2,000 ng |
| Processing time | <5 seconds/sample |
The Agilent 2100 Bioanalyzer system is an established automated electrophoresis solution for the sample quality control of biomolecules. The system integrates an instrument, data processing software, reagents, and a microfluidic chip specific for DNA, RNA, or protein analysis. It is suitable for next-generation sequencing (NGS), gene expression, biopharmaceutical, and genome editing workflows, delivering highly precise analytical evaluation of various sample types. Advantages of microfluidics-based automated electrophoresis over traditional gel electrophoresis include dramatically reduced sample (1 µL for nucleic acids, 4 µL for proteins) and reagent consumption, significantly faster analysis time, and less hands-on activities during sample preparation and data analysis.
Assays
High Sensitivity DNA kit
For the separation, sizing and quantification of dsDNA samples of limited abundance and sized from 50 – 7000 bp.
| Quantitative range | 5-500 pg/µL |
| Quantitative reproducibility | 2000-7000 bp: 10 % CV |
| Sample volume | 1 µL |
| Samples per chip | 11 |
| Sizing accuracy | ± 10 % |
| Sizing range | 50-7000 bp |
| Sizing resolution | 600-7000 bp: 20 % |
RNA 6000 Pico kit
For the analysis of RNA samples of limited abundance down to 50 pg/µl of total RNA or 250 pg/µl of mRNA.
| Qualitative range | Total RNA in water: 50-5000 pg/µL, mRNA in water: 250-5000 pg/µL |
| Quality score of sample | RIN |
| Quantitative accuracy | ±30 % |
| Sample volume | 1 µL |
| Samples per chip | 11 |
RNA 6000 Nano Kit.
For the analysis and quantitation of total and mRNA samples of 25 to 500 ng/µL in concentration.
| Qualitative range | Total RNA: 5 – 500 ng/µL, mRNA: 25 – 250 ng/µL |
| Quality score of sample | RIN |
| Quantitative accuracy | ±20 % |
| Quantitative range | Total RNA: 25 – 500 ng/µL, mRNA: 25 – 250 ng/µL |
| Sample volume | 1 µL |
| Samples per chip | 12 |
The 5200 Fragment Analyzer system is a parallel capillary electrophoresis instrument that improves lab efficiency by allowing you to separate 12 samples in parallel (one is ladder).
The 5200 Fragment Analyzer system performs DNA and RNA quality control (QC) for a broad range of samples, including gDNA, small RNA, cfDNA, large DNA fragments, total RNA, and mRNA. The instrument is ideal for individualized workflows, including library QC for next generation sequencing (NGS) and mRNA integrity analysis.
Features
Offered Assay
HS NGS Fragment Kit (1-6000bp) Fragment Analyzer system kit for the quantitative and qualitative analysis of NGS libraries and intermediates from 100 to 6000 bp at low concentrations.
| DNA sizing range | 100 – 6000 bp |
| Fragment sensitivity range | 5 – 500 pg/µL |
| Quantitative accuracy | ± 25 % |
| Sample volume | 2 µL |
| Sizing accuracy | ± 5 % |
| Sizing resolution | 1000-6000 bp:≤ 10 % |
| Smear sensitivity range | 50 – 5000 pg/µL |
RNA kit (15NT) – Fragment Analyzer system kit for the quantitative and qualitative analysis of total RNA from 200 to 6000 nt.
| Detection limit | 5 ng/µL |
| Qualitative range | Total RNA: 5 – 500 ng/µL; mRNA: 1 – 100 ng/µL |
| Quantitative accuracy | ± 20 % |
| Quantitative range | Total RNA: 25 – 500 ng/µL; mRNA: 20 – 100 ng/µL |
| Sample volume | 2 µL |
| Sizing accuracy | Total RNA: ± 5 %; mRNA: ± 10 % |
Other kits by arrangement
| Document | EN manual |
The CM1950 is a high-performance cryostat with an encapsulated microtome and separate specimen cooling. It features a UV disinfection system, an integrated extraction system for section waste and an motor for motorized sectioning. The cryostat is designed to produce frozen sections for biological, medical and industrial applications.
| Section thickness range | Setting values 1 to 100 µm 1.0 µm – 5.0 µm in 0.5 µm steps 5.0 µm – 20.0 µm in 1.0 µm steps 20.0 µm – 60.0 µm in 5.0 µm steps 60.0 µm – 100.0 µm in 10.0 µm steps |
| Trimming range | 1 – 600 µm (research) 1,0 µm – 10,0 µm in 1,0 µm steps 10,0 µm – 20,0 µm in 2,0 µm steps 20,0 µm – 50,0 µm in 5,0 µm steps 50,0 µm – 100,0 µm in 10,0 µm steps 100,0 µm – 600,0 µm in 50,0 µm steps |
| Maximum specimen size | 50 x 80 mm |
| Total specimen feed | 25 mm |
| Vertical specimen stroke | 59 mm |
| Specimen retraction | 20 µm or off |
| Specimen orientation | 8° (x-, y-axis), 360° rotation of specimen disc |
| Electric coarse feed | Slow: 300 µm/s, in 20 µm steps Fast: 900 µm/s |
| Cryochamber | Temperature range: 0°C to -35°C |
| Specimen cooling | Temperature range: – 10 to – 50 °C |
| Defrosting of specimen head | manual defrost |
| Cryochamber defrosting | Automatic cryochamber defrosting: programmable, (hot gas defrost), selectable time, 1 defrost in 24 h or manual hot gas defrost, Defrost time: 12 minutes Automatic shut off defrost: at – 5 °C chamber temperature |
| Quick-freeze shelf | Minimum temperature: down to – 42 °C, at chamber temp. – 35°C Number of freezing stations: 15 + 2 Defrost: manual hot-gas defrost |
| Peltier element | Number of freezing stations: 2 Maximum temperature difference: 17 K, at chamber temp. of – 35 °C |
| Documents | EN manual CZ manual |
The ME220 focused-ultrasonicator is the multi-sample, multi-application benchtop sample preparation solution. Capable of 1 to 8 sample batch processing at the bench-top, single tube sample processing capacity with NGS sample volumes of 15 to 130 µl. Ideal for DNA/RNA shearing, cell lysis and tissue lysis followed by DNA/RNA/protein extraction. With 20 W average incident power, it is ideal for cell lysis, cfDNA extraction from plasma, DNA extraction from dried blood spots, DNA/RNA/chromatin shearing, DNA/RNA/Total NA/protein extraction from FFPE, and tissue lysis.
The Diagenode Bioruptor uses a gentle method of sonication to retain the integrity of DNA and/or biological complexes, including chromatin, protein-protein binding, protein-DNA complexes, and other biochemical and biological assay systems. The Bioruptor Sonication System uses a waterbath to generate these indirect sonication waves, which emanate from an ultrasound element below the water tank.
Because the system is gentler than other sonicators, many customers report better and more consistent results with the Bioruptor than with harsher sonication methods. Multiple closed tubes can be sonicated together and the continuous rotation of tubes allows even distribution of the energy for efficient sonication. The Bioruptor enables automation of sonication, guaranteeing higher reproducibility of results.
