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Automated High Yield Extraction of gDNA from Plant Samples

Tecan
25 Mar 2016

This application note demonstrates the potential for high yield gDNA extraction using the MACHEREY-NAGEL NucleoSpin® Plant II Midi kit on a Freedom EVO® platform. Plant research is often geared towards crop improvement, and focuses on yield and robustness to pathogens and other stress factors, such as heat or draught. It is often necessary to sequence the genome, creating the need for purification of high quantities of gDNA. DNA extraction from plant material is therefore an integral step in plant research.

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Freedom EVO® NGS Workstation

Tecan

The Freedom EVO NGS workstation combines Tecan’s expertise in laboratory automation with sequencing-verified protocols to offer hassle-free NGS sample prep at the touch of a button. NGS is the fastest growing application in genomics, yet many sample preparation protocols can be labor intensive and time consuming. The Freedom EVO NGS workstation has been developed to offer robust and reliable automation of library preparation, quantification, qPCR set-up, normalization, pooling and capture. Offering user-friendly, walkaway automation at the touch of a button, it eliminates the need for extensive manual processing, helping to simplify day-to-day activities and ensure high quality results. Freedom EVO NGS workstation includes all the modules required for precise set-up of NGS sequencing libraries and, with one-touch method selection and step-by-step user instructions via Tecan’s intuitive TouchTools™ graphical interface, it reduces hands-on time and increases productivity – even for inexperienced users. The system’s key benefits include: Precise pipetting – from 1,000 µl down to 0.5 µl using eight pipetting channels and innovative air displacement pipetting technology Integrated temperature control – to keep reagents cool and provide optimal enzymatic conditions Efficient bead clean-up –  using a 96-position magnetic plate separator (Alpaqua 96S Super Magnet Plate) Walkaway processing – with on-board consumables storage for long unattended runs Straightforward operation – with step-by-step set-up instructions To further streamline processing, Tecan has worked with leading industry partners to supply ready-to-run protocols for a number of popular NGS technologies. Protocols for Illumina’s TruSeq™ Nano DNA, TruSeq Stranded mRNA* and Nextera™ Rapid Capture Exome* chemistries have been developed in collaboration with Illumina and the High-Throughput Sequencing Facility, University of North Carolina at Chapel Hill, with thorough testing and sequencing data analysis to ensure high quality results. In addition, the system is supplied with protocols covering the Ion Torrent™ library preparation workflow for Ion AmpliSeq™ panels, developed and supported by Thermo Fisher Scientific. *Illumina-qualified protocol.

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Freedom EVO® PCR Workstation

Tecan

The Freedom EVO PCR workstation is a fully scalable, modular system offering flexible automation for PCR set-up and cycle sequencing reaction preparation.

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Sample PreparationSample preparation can improve the quality and speed of separation techniques. Products to assist sample preparation include filtration equipment, evaporators, membranes and sieves.Genome AnalysisGenomics, the study of genomes, includes functional genomics, evolutionary genomics and comparative genomics. There are many genomic technologies such as DNA sequencing of whole genomes, computational biology and bioinformatics. DNA and nucleic acids must be isolated and concentrated from cells for analysis with kits, automated analyzers and software. Other useful technologies for studying genomics include PCR, microarrays and electrophoresis.MicroplatesMicroplates are multi-well plates used to increase the throughput of biological investigations. The number of wells microplates contain can range from 6 to 3243 wells, with the 96-well format being the most commonly used. Microplates can come tailored for a range of applications including cell culture, PCR, filtration, storage, non-binding surface, protein crystallization, as well as pre-coated, deep well and normal Standard microplates. Additionally, options for microplate colors include clear , black, white or black with clear bottom and white with clear bottom for absorbance microplate reader applications. Find the best microplates for your lab in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.High-Throughput ScreeningHigh-throughput screening (HTS) is an automated drug discovery technique for identification of active compounds against a compound library. Use HTS readers and integrated assay preparation / analysis workstations to screen your compounds. Identify active compounds against various HTS libraries, including membranes, proteins and peptides and HTS cell lines. Find the best high-throughput screening products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.PCR and Thermal CyclingPolymerase chain reaction (PCR) kits and thermal cyclers are used for the in vitro amplification of DNA permitting subsequent analysis and experimental procedures. Explore a range of high-quality polymerase, primers and nucleotides or simplify your workflow with a PCR mastermix. Find reverse transcription PCR (RT-PCR) and cDNA synthesis kits for RNA products and libraries. Quantitatively measure the amplification of DNA with real-time PCR (qPCR) and droplet digital PCR (ddPCR) kits and systems, and discover automated PCR setup solutions to increase throughput. Alternative DNA amplification methods also include recombinase polymerase amplification (RPA) kits. Find the best PCR kits and thermal cyclers and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Sample ManagementSample management systems include sample storage devices such as freezers and plate storers, sample environment enclosures and sample organization, retrieval and sorter systems. Useful system features include high-throughput, automation, robotic arms, automated liquid handling and associated database systems. Accessories in sample management include barcode scanners, heat sealers and tubes.DNA / RNA Extraction and PurificationPurified DNA and RNA are required for numerous downstream molecular biology applications. Consequently, the importance of high-quality DNA/RNA extraction and purification equipment cannot be underestimated. Many purification kits are available and are typically optimized for nucleic acid type and source, including plasmid DNA, genomic DNA, mRNA, RNA and viral nucleic acid purification kits. Automated extraction and purification of nucleic acids can be implemented with magnetic bead separator instruments or high-throughput purification workstations. Find the best DNA/RNA extraction and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.DNA SequencingDNA sequencing, such as sanger sequencing, is a biological technique that determines the precise order of nucleotide bases in a fragment or template of DNA. DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Gene Expression and Molecular CloningMolecular cloning is a set of techniques that utilizes vectors to transfer recombinant DNA into host cells and is an essential tool for investigating the expression of genes and proteins in bacterial or mammalian cells. A variety of vectors optimized for gene cloning and expression in a range of host organisms are available, alongside competent cells for genetic replication. Here, you can explore a range of molecular tools, high-quality genomic and cDNA libraries, premade clones, transformation and transfection reagents and mutagenesis or gene expression detection assays and expression arrays. Find the best gene expression and molecular cloning products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Robotic InstrumentsRobotic instruments can be used for high-throughput automation of many lab processes. Such processes use instruments for assays like cell based assays and ELISA, for sample preparation like shakers, centrifuges and incubators, and for analysis such as sequencing and western blot analyzers. Useful features of robotic instruments include speed, reproducibility, barcode readers, software and automation.Robotic WorkstationsRobotic workstations are automated platforms enabling the user to perform high-throughput, multi-application processes, from sample preparation tasks such as PCR set-up, DNA purification and NGS library preparation, to integrated sample prep and analysis workstations. Automation makes processes consistent, fast, precise and fully walk-away. Find the best robotic workstations in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Software PlatformsSoftware platforms are useful for various stages of laboratory experiments from data collection to data storage and processing. For instance lab software is available for system control, data management, data analysis and qualification / validation.Plate ProcessingAutomated plate processing is used in microplate technologies for high-throughput, speed and efficiency. Plate processing systems include microplate handlers for moving plates, heat sealers, stackers and carousels for storage, retrieval and delivery, microplate washers and piercers. Useful features of plate processors include walk-away automation, compatibility and easy integration with microplate systems.Automated Liquid HandlingAutomated liquid handling equipment is used to mix, dilute and dispense allotted volumes of liquid into microplates and other vessels automatically. The robotic, liquid handling arms can dispense from single channel to 3456 multichannel as well as operate nanoliter dispensing, enabling high throughput of samples. Find the best automated liquid handlers in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.

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