Genomics

In general, genomics studies structure and function of genomes of biological organisms by tools of molecular biology, and is usually divided into structural, functional and systematic genomics. Most popular structural genomics studies nucleotide sequences, their modifications, interaction with proteins, etc.; functional genomics explores the realization of genetic information; and systematic genomics examines genetic sequences for in order to determine systematic station of biological species.

Our center provides modern equipment for different genomic techniques. The center supports the possibility of sequencing on different platforms, including Sanger (capillary) sequencing, being the classical method of sequencing which allows to perform several sequence analyses at a time, and massive parallel sequencing of the next generation (NGS) being available on two platforms – Roche 454 GS Junior and ABI Ion Torrent. The center also provides the complementary equipment for NGS library construction.

The center is equipped with the wide variety of PCR machines allowing to perform different types of PCR analysis, including quantitative PCR (qPCR), and genetic typing. Specialists in the center consult users and help them to correctly choose the proper platform and consumables, as well as to design the whole experiment and its separate steps, and to process the data acquired. E.g., the digital PCR (DD-PCR) suits best for searching the single-nucleotide polymorphism (SNP) and for performing the quantitative PCR. The microfluid system of the high-performance PCR (Fluidigm) is usually the choice for the research works with big number of gene expression measurements.

For the location of the investigated genetic processes, which is widely used in the developmental biology and neurobiology, our center offers robotics technology for performing the fluorescence in situ hybridization (FISH). The complex of laser microdissection equipment allows to analyze different areas of interest within the sample.

Apart from the analytical equipment, various software is installed in the center for the data analysis.

Sequencing

  • ABI PRISM 310 Genetic Analyzer

The ABI PRISM 310 Genetic Analyzer is an automated single-capillary genetic analyzer. It allows to perform different types of sequencing and fragment analysis such as comparative sequencing, including de novo sequencing, SNP discovery and validation, linkage analysis, and mutation detection. The instrument supports most gel-based assays. For more information visit www.lifetechnologies.com.

  • ABI PRISM 3500xL Genetic Analyzer
In contrast to the 310 Genetic Analyzer, the 3500xL Genetic Analyzer is designed on the basis of the 24-capillary platform. It has significally improved the throughput, intracapillary and intradevice repeatability and dynamic range. For more information visit www.lifetechnologies.com.
  • Roche 454 GS Junior Sequencing System
The GS Junior system is designed on the basis of the 454 Sequencing Technology and provides the proven long-read sequencing. The instrument allows to perform the amplicon sequencing, sequence capture, whole genome sequencing (including de novo sequencing and resequencing of microbial organisms), characterization of complex environmental samples, pathogen discovery, and full-length sequencing and de novo assembly of transcripts.  For more information visit www.gsjunior.com
  • ABI Ion Torrent PGM Sequencer
The Ion Personal Genome Machine (PGM) is the next generation sequencer based on the semiconductor chip technology. In contrast to other sequencers, the Ion PGM sequencer provides the fastest run times along with the high accuracy and long reads. For more information visit www.iontorrent.com

PCR

  • Bio-Rad C1000 Thermal Cycler
The C1000 Thermal Cycler is a standard PCR machine designed on the fully modular flexible platform being able to accommodate different throughput needs with easily interchangeable reaction modules. It allows to perform amplification reactions, cloning, cycle sequencing, gene expression and mutagenesis studies. The  presence of the thermal gradient provides quick and easy identification of the annealing temperatures. For specifications visit www.bio-rad.com
  • Bio-Rad CFX96 Real-Time PCR Detection System
The CFX96 Real-Time PCR Detection System is complex device combining a standard C1000 thermal cycler with the 6-channel module of fluorophore detection. The instrument allows to perform real-time PCR with the precise thermal control due to the special thermal gradient technology. For more information visit www.bio-rad.com.

High-Performance PCR

  • Microfluidic PCR device Fluidigm BioMark HD
The BioMark HD System is a real-time PCR instrument based on fast PCR-enabled nanofluidic technology. It allows to perform unparallel multiple real-time PCR reactions and digital PCR, combining thermal cycling and fluorescence detection on Integrated Fluidic Circuits which significantly increases productivity. The device can also be used to perform analysis of gene expression, genotyping, digital PCR, mutant detection, etc. For more information visit www.fluidigm.com.
  • Bio-Rad QX-100 Droplet Digital PCR System
The droplet digital PCR (ddPCR) is the third generation of PCR technologies which allows to measure the absolute quantity of the target DNA with the highest precision of 1 molecule. The device also provides the possibility to detect rare DNA copies, measure small fold differences and the variation of the number of copies, perform mutation detection, gene expression analysis of rare transcripts and miRNA analysis as well. For device specifications visit www.bio-rad.com.

Software

  • DNAStar Lasergene 10 Software
Lasergene software is the complex of several applications aimed at the comprehensive analysis of genome, such as DNA, RNA and protein sequence analysis. Using the Lasergene software researchers can construct contigs and scaffolds, form physical maps, analyze mutations and different variations, etc. For more information visit www.dnastar.com.

Functional Genomics

  • Liquid robotics system Tecan GenePaint Evo 150/4
The GenePaint Evo 150/4 is the robotic workstation designed to handle repetitive liquid transfer tasks. The workstation comprises the flexible robotic 4-channel liquid handling tool of variable volume and independent processing. It can be used in different fields of biological investigations and allows to perform immunostaining and in situ hybridization reactions (including fluorescence in situ hybridization), nucleic acid extractions, enzyme-linked immunosorbent assays, serial dilutions, MALDI spottings, etc. For specifications visit www.tecan.com.
  • Leica LMD7000 laser microdissection system
Leica LMD laser microdissection system provides laser-based microscopic dissection of regions of interests of biological samples with the precision of single cell from all types of tissues and cell cultures, and subsequent contamination-free collection of the homogeneous ultra-pure sample. For specifications visit www.leica-microsystems.com.

Complementary Equipment

  • Bio-Rad CHEF MAPPER XA Pulsed Electrophoresis System
The CHEF MAPPER XA System is a pulsed field gel electrophoersis (PFGE) system constructed on the basis of the FIGE and AFIGE technologies resulting in the superior resolution from 100 bp to 10 Mb. The instrument can be used for all PFGE applications. The user can choose any pulse angle from 0 to 360°, which allows optimal separation of both chromosomal and plasmid DNA. The nonlinear ramps allows to separate fragments linearly from 50 to 700 kb. For more information visit www.bio-rad.com.
  • Bio-Rad Gene Pulser Xcell Electroporation System
The Gene Pulser Xcell system is a modular electroporation system composed of the main unit, the cuvette chamber, the capacitance extender and the pulse controller. The instrument allows to transfect all cell types from primary and stem cells to bacteria and yeast. For specifications visit www.bio-rad.com.
  • Beckman Coulter Optima L-100XP Preparative Ultracentrifuge
BC Optima L-100XP preparative ultracentrifuge is designed for both special and routine tasks of the separation, isolation and sedimentation of different compounds, cells and subcellular fractions applied in various research works in genomics, metabolomics and proteomics. The ultracentrifuge is equipped with three rotors (Type 100 Ti, SW 32 Ti and Type 25 Rotor) for different volume tubes. For more information visit www.beckmancoulter.com.
  • Beckman Coulter Avanti J-30I Centrifuge
BC Avanti J-30I is the maximum g-force high-performance fully automatic floor centrifuge. It provides fast separation forces of 100000 x g at speeds up to 30000 rpm for volumes up to 4 liters or 10 microplates per run. The centrifuge allows separation of homogeneous tissues components, isolation of cell membranes on a density gradient, separation and fractioning of cellular organelles, DNA isolation on microplates, protein sedimentation, purification of the culture medium by cell debris sedimentation. For specifications visit www.beckmancoulter.com.
  • Labconco CentriVap Centrifugal Vacuum Concentrator
CentriVap concentrator is a benchtop vacuum concentrator designed to rapidly concentrate biological substances in both water and alcohol solutions in a wide variety of temperatures using the combination of centrifugal force, vacuum and heat techniques. For more information visit www.labconco.com.
  • Microchip Electrophoresis System for DNA/RNA Analysis Shimadzu MCE-202 MultiNA
The Shimadzu MultiNA is a next-generation microchip capillar electrophoresis system being a replacement for manually-prepared agarose gel electrophoresis solving most of its problems. The Shimadzu MultiNA is a fully automated machine designed for automatic scheduled high-speed up to 120 sample analysis of DNA/ RNA size prediction and quantitation. The mashine excludes hazards associated with ethidium bromide staining, instead using SYBR-family dyes. For more information visit www. shimadzu.com.
  • Agilent 2100 Bioanalyzer
Agilent 2100 is a capillar electrophoresis system designed on the basis of the microfluidics platform. It allows to perform sizing, quantification and quality control of DNA, RNA, proteins and cells. The device automates processes of gel application on microchips, molecule separation in the direct current field, detection and analysis of the obtained results. For more information visit www.agilent.com.
  • Sage Pippin Prep DNA size selection system
The Pippin Prep is an automated preparative electrophoresis system which provides electrophoretic separation and extraction of DNA fragments of different size. Using different pre-cast and disposable gel cassettes, the system detects DNA fragments from 50 bp till 8000 bp according to the size range without exposure to the harmful X-rays and collects DNA fractions directly into the buffer. The throughput of the instrument is 4 DNA samples per run, being separated without any cross-contamination. For specifications visit www.sagescience.com.
  • Hamilton REM e STARlet Liquid Handeling Workstation
REM e STARlet Liquid Handling Workstation is a fully automated system for emPCR enrichment and sequencing primer hybridization for the parallel sequencing performance using vortexing, vacuum filtration, magnetic bead capture and heating. The workstation is designed to support the Roche 454 GS Junior Sequencer. For more information visit www.hamiltonrobotics.com.
  • ABI Ion One Touch Robotics System
The Ion One Touch robotics system provides fast and automated template preparation for the ABI Ion Torrent PGM sequencer.
  • Diagenode BioRuptor UCD-200 DNA Fragmentation System
The BioRuptor system provides ultrasonic DNA fragmentation and microparticle disaggregation. BioRuptor has a throughput of 12 0.5ml samples per run in the automatic mode. For more information visit www.diagenode.com.
  • MPbiomed FastPrep-24 Homogenizer
The FastPrep-24 instrument is a high-speed benchtop homogenizer providing the fast homogenization of biological samples of any solidity without redundant heating. More specifications visit www.mpbio.com.
  • Routine electrophoresis systems
© Research resource center for molecular and cell technologies, SPbSU, 2012-13