Tataa Biocenter - Laboratories and instruments

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TATAA Genomics Core Facility

Core Facility areas

Laboratories and instruments

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Laboratories and instruments

Make good use of our laboratories and unique instrument park at TATAA Biocenter

TATAA Biocenter's laboratories and unique instrument park has the latest equipment for extraction and quality control of nucleic acids, cDNA synthesis, real-time PCR quantification and post-PCR analysis. We are prepared for a seamless workflow, with all instrumentation necessary for performing well designed experiments and for optimal handling of samples with specific requirements.

Our instrument park is available for use within our commissioned research projects and services. Also, our TATAA Genomics Core Facility service offers you to use our equipment for your own experiments to be able to perform all aspects of real-time PCR and its sample preparation.

Click here for instruments available at TATAA Biocenter Prague, Czech Republic
Our facility in Göteborg:

LABORATORIES

Our facility at TATAA Biocenter Göteborg is divided into separate labs to prevent contamination. We have five different labs:

Sample Preparation lab
Nucleic acids are extracted in the Sample Preparation lab, and also tested for quality and quantity. When there is a risk for hazardous fumes the Air Curtain Cabinet can be used. This lab contains several systems for nucleic acid extractions as well as for quality and quantity testing. General lab equipment include two heating blocks, centrifuges and a vortex.

Pre-PCR lab
The Pre-PCR lab is a DNA-free zone. Here primers and probes are diluted and mastermixes are prepared. The preparations are made in a DNA-free hood, kept clean using UV-light. In the Pre-PCR lab there is also a scale to weigh e.g. chemicals and components of buffers etc.

PCR lab
In the PCR lab all PCR reactions are set up. Samples are diluted, templates and mastermixes are mixed and transferred to plates, strips, tubes etc. Also, here the real-time PCR is perfromed. In addition to several automated liquid handling systems and the real-time PCR instruments, general equipment include centrifuges, vortexes and a heatsealer.

Post-PCR lab
The Post-PCR lab is used for work with PCR products. Here we can purify and dilute PCR products for downstream work or confirm the specificity of your assays by gel electrophoresis.

Cultivation lab
The Cultivation lab holds the possibility for cultivating bacteria and yeast in small scale. The equipment is e.g. shakers and heating cabinets.

NUCLEIC ACID EXTRACTION AND QUALITY CONTROL

Agilent 2100 BioAnalyzer

The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells. Up to 12 samples can be run simultaneously and 2 µl of the sample is enough to load to each well on the chip. In 30-40 minutes the run is ready and you can analyze your obtained data. With the RIN algorithm (RNA Integrity Number) you get a number of the quality of your RNA sample.

Bio-Rad Experion Automated Electrophoresis System

Experion automated electrophoresis station performs all of the steps of gel-based electrophoresis in one compact, durable unit. It separates, stains, destains, detects bands, and makes the images and data analysis. The system requires as little sample as 2 µl sample and up to 12 samples can be analyzed in one run. Reproducible separation of protein and nucleic acids can be accomplished in 40 minutes. At TATAA Biocenter the system is often used for analysis of integrity of RNA and DNA samples by looking at 18S and 28S ribosomal RNA.

FujiFilm QuickGene-810
QuickGene-810 is a semi-automated system for extraction of RNA and DNA. The system is build with an 80µm membrane film and rapidly isolates the RNA/DNA from various samples with high quality yields. The membrane technique requires no centrifugation giving less strain on samples. The QuickGene can handle up to 8 samples at a time.

FujiFilm QuickGene-Mini80

QuickGene-MINI80 is the smaller brother of QuickGene-810. The compact system shares the extraction mechanisms and kits with QuickGene-810 but is a smaller system where you easily push the liquid through the columns by turning the wheel on the instrument.

Lab901 ScreenTape R6K System

ScreenTape R6K analyzes RNA and DNA without any gel preparation or chip priming. 1-96 samples can be loaded, separated, imaged and analyzed in only one minute per sample (batch prepare all 96 samples and run them in 2 hours). This automated platform calculates the Screen Tape Degradation Value (SDV, equivalent to RIN) through mathematical analysis of the RNA profile, which allows objective quality scoring of eucaryotic total RNA.

NanoDrop ND-1000 Spectrophotometer

The NanoDrop^TM 1000 Spectrophotometer enables highly accurate UV/Vis analyses of samples with remarkable reproducibility. The patented sample retention system eliminates the need for cuvettes and capillaries which decreases the measurement cycle time. In addition, the high absorbance capability eliminates the need for most dilutions. The ND-1000 is an excellent instrument to measure the concentration of DNA, RNA and protein. To some degree, purity from phenol and proteins in RNA samples can also be evaluated. The NanoDrop uses only about 1-2 µl of the sample and there is no risk of contamination of the original sample.

NanoDrop ND-3300 Fluorospectrometer
NanoDrop ND-3300 makes a broad spectrum fluorescence analysis quick and easy. It uses fluorescence emission (400-750 nm) for measuring fluorophores and reagents in samples as small as 1 µl. UV, Blue and White LED excitation covers a broad wavelength range and makes it possible to analyze multiple emission profiles from a single sample.

Qiagen TissueLyser
The TissueLyser disrupts multiple biological samples through high-speed shaking in plastic tubes with stainless steel, tungsten carbide, or glass beads. Up to 48 samples can be processed at the same time. The instrument at TATAA is often used for efficient homogenization for tissue samples.

Sigma 1-14 centrifuge - for spin columns
This high speed small-footprint microlitre centrifuge is suited for centrifuging 24x 1.5/2 ml tubes, great to use during extraction with spin columns. The acceleration and deceleration times are short. The maximum spin is 14 800 rpm/16 162 x g. It is easy to handle with big buttons and bright LCD display.

LIQUID HANDLING

BioTX WellAware Pipetting Systems

These personal automation systems use the BioTX Lab Suite softwares four modules to automate many common laboratory tasks. The WellAware Module is for the setup of sorting and hit picking operations, and for the pipetting of electronic Standard Operating Procedures (eSOPs) made in other modules. The WellAware Module with a PC, monitor and footswitch allows for light and voice guided manual pipetting or sorting of an eSOP. The Protocol Module is used to generate eSOPs for PCR, Sequencing, ELISA and Genotyping protocols. The Norm Module is for eSOP setup of DNA & protein normalizations and for serial dilutions. The Labeling Module is for the printing of barcode labels for vials, plates and other items.

Corbett Robotics CAS-1200

CAS-1200 pipetting station allows you to rapidly and reliably perform your pipetting automatically, preventing human mistakes. The station uses a single-channel pipette to automate PCR setup, e.g. distribute mastermixes and add samples. Up to 96 PCR reactions can be set up in approximately 30 minutes.

The instrument worktable is set up with a Master Mix Block, a Reagent Block, tips, and plates/tubes. Conductive tips enable high-precision pipetting with liquid level sensing. The software, which is operated on a PC next to the robot, is easy to learn and use. During the run the position of the pipetting head is highlighted on the screen as it moves, allowing the progress of a run to be followed in real-time. A feature that allows samples concentrations to be imported to the software directly from a text file is excellent when normalizing RNA or DNA concentrations. Other helpful features can be used when performing serial dilutions with variable dilution ratios or optimizing assays.

Eppendorf epMotion 5070

The Eppendorf epMotion 5070 is an automated pipetting system which enables fast and reproducible liquid handling by pipetting and dispensing. Pipetting protocols previously carried out manually can easily and quickly be transferred to the epMotion 5070 workstation. The workstation is programmed using an integrated control panel. By prompting the user to carry out necessary actions, programs are easy to follow and understand. The epMotion 5070 workstation enable quick filling of plates e.g. in the 384-well format. Optical sensors control and ensure the reliability of the procedure.

QUANTITATIVE REAL-TIME PCR INSTRUMENTS

Applied Biosystems 7500 Fast Real-Time PCR System

The Applied Biosystems 7500 Fast Real-Time PCR System offers maximum performance in minimum time. Fully optimized for Fast cycling, the 7500 Fast delivers high-quality results in as little as 30 minutes. The specially designed Fast block ensures thermal uniformity at top speeds and fast optical plates ensure excellent precision in 10-30 uL reaction volumes.

Applications include:

Gene Expression Analysis
Pathogen quantitation
SNP genotyping
Isothermal and +/- assays utilizing internal
positive controls

The Applied Biosystems High Resolution Melting (HRM) Software enabels real-time PCR melt curve assays to be used more accurately for mutation scanning and genotyping. Use the software to perform more sophisticated melting analysis with an easy to follow workflow and minimal subjective data analysis steps.

The HRM Software:

Shortens analysis time by auto-calling genotypes and automatically omitting the no template controls
Minimizes subjective analysis by automatically grouping unknown variant clusters
No temperature shift required - distinguish between homozygous mutants and wild type more easily
Allows easy data review with customizable multi-plot views, expandable windows and one-click color assignment to highlight curves of interest

Applied Biosystems OpenArray® Real-Time PCR Platform

The OpenArray® Real-Time PCR System is a high-throughput system which combines hundreds of samples per day without robotics. The plate format enables testing from 48 samples against 18 unique assays to 12 samples against 224 unique assays. The system workflow includes real-time thermocycling and fluorescence imaging of TaqMan and SYBR assays. The Open Array instrument uses three filtered high-brightness LEDs to excite, and a cooled CCD camera to detect the fluorescence emissions from dyes. The software allows user to acquire, analyze, and manage data quickly and easily. Data from many OpenArray Plates may be combined into the same data project.

It is possible to order plates with preloaded assays and just add sample and mastermix before run.

With the OpenArray system TATAA Biocenter offers Digital PCR services, as well as High-throughput real-time quantitative PCR (qPCR) analysis services.

Bio-Rad CFX96 Real-Time System

Please note that the CFX96 is not always present at the Gothenburg office. If needed, the instrument can be requested. Notify your TATAA contact if you wish to use the instrument.

The CFX96 optical reaction module converts a C1000 thermal cycler into a powerful and precise real-time PCR detection system. This six-channel real-time PCR system combines advanced optical technology with precise thermal control to deliver sensitive and reliable detection.

Features include:

Factory calibration to minimize setup time
Data collection from all wells during data acquisition
Multiple data acquisition modes, including a 1-color fast scan for SYBR Green users
Thermal gradient feature to optimize reactions in a single run
CFX Manager software with advanced analysis tools for performing normalized gene expression
Optimized design lets you configure the CFX96 system to fit your laboratory needs - run without a computer, run up to 4 systems from 1 computer, or integrate with the CFX automation system for higher throughput
Email notification option that sends an email, with an
attached data file, upon run completion

Corbett Rotor-Gene 6000

Rotor Gene 6000 combines multiple optimized design features to provide the outstanding performance and reliable results that your research demands. The unique centrifugal rotary design of the Rotor Gene 6000 makes it a precise and versatile instrument with an outstanding thermal and optical performance. Each tube spins in a chamber of moving air, keeping all samples at precisely the same temperature during rapid thermal cycling. Detection is similarly uniform. When each tube aligns with the detection optics, the sample is illuminated and the fluorescent signal is rapidly collected from a single, short optical pathway. The platform can run 36 or 72 tubes at a time. The format is easily changed.

The software allows you to create new excitation/detection wavelength combinations, which means that the Rotor Gene 6000 is compatible with dyes you may use in the future.

The rotary design of the Rotor Gene 6000 is also highly suited to HRM. The platform is capable of deciphering the most difficult class IV SNPs by HRM.

The rotary design delivers:

Well-to-well variation below ±0.01°C (20 times less than block cyclers)
Uniform detection eliminating the need for ROX reference dye
Fast ramping and negligible equilibration times for short run times
Complete confidence in your results!

Eppendorf Mastercycler ep realplex⁴real-time PCR system

Small, fast and flexible - the Mastercycler ep realplex real-time PCR system meets all the latest requirements of quantitative PCR applications. Fast temperature ramping, short

detection times and intuitive assay programming. The 96 well format is flexible and this completely open system allows you to use tubes, plates and reagents of your choice. The instrument at TATAA contains the ultrahigh-speed gradient S block and realplex⁴ module which can be used for multiplexing. The system is compatible with nearly all fluorescent dyes on the market. The Innovative Eppendorf Thermal Sample Protection technology prevents premature heating of the samples, which significantly reduces the amplification of nonspecific PCR products during this heating phase. A solid construction with minimal moving parts makes this a quiet, dependable unit that promotes consistently high sensitivity in your real-time PCR experiments.

Roche LightCycler 480 Real-Time PCR System

The LightCycler ^® 480 Real-Time PCR System is a high throughput gene quantification or genotyping real-time PCR platform. With exchangeable blocks for 96 and 384 samples in multiwell plates the instrument is nice to use when handling small amounts of samples as well as large amounts. The LightCycler ^® 480 Real-Time PCR System can complete a 348

well PCR run in 40 minutes. The system is operated by a separate desktop data station based on Windows XP. The intuitive software includes step saving short cuts for high-throughput sample and data handling. One-click experiment set up with options to refine results later.

The platform gives options for basic and advanced gene expression analysis. Work in a broad dynamic range from 10¹⁰ to a single copy in a single run is possible. Examples of projects to perform on the platform are genetic variation studies based on hybridisation probes, simple probes or hydrolysis probes. LightCycler®480 is highly robust and convenient when working with mutation discovery. The features for High Resolution Melting is useful for reducing time and costs compared to non- homogenous mutation screening methods that require PCR and analysis on separate instruments. The platform provides an outstanding specificity and sensitivity with high sample throughput.

Stratagene Mx3005P

The Mx3005P software is easy to use due to the intuitive interface, quick experiment design, powerful data analysis and easy report generation.

Due to the flexibility the systems are ideal for a wide variety of applications and chemistries. For example:

Gene Expression Analysis
Microarray Data Validation
SNP Genotyping
Pathogen Detection

MISCELLANEOUS

Air Curtain Cabinet

When extracting nucleic acids with volatile compounds at TATAA Biocenter the work is performed in an air curtain cabinet to avoid breathing in the fumes. The cabinet uses dual air curtain technology creating a rotation of the air mass inside the cabinet, preventing the fumes from escaping. It also gives the operator the freedom of an open front cabinet to work in.

Eppendorf centrifuge 5804
The bench-top centrifuge 5804 from Eppendorf is a multi-purpose centrifuge feature a powerful, main-tenance free motor. A variety of rotors for different applications are available. It is possible to centrifuge plates for the qPCR applications as well as high volume centrifugation of Falcon® tubes just by changing the rotor. The rotor spins up to 14 000 rpm, 20 800 x g.

FlashGel DNA System

The FlashGel® System is a fast way to separate DNA and the only way to watch DNA migration as it happens. The system consists of enclosed disposable, precast agarose gel cassettes and a combined electrophoresis and transilluminator unit. Monitor gel runs right at the bench, without UV light. The DNA seperates in 2- 7 minutes.