Lab Automation References - HSE•AG's Know-How

We have been at the leading edge of lab automation for 20 years and have developed revolutionary systems for a wide range of application areas. In addition to this, we have optimized products with technical advancements, successfully prepared products for industrialization and serial production, and carried out life cycle management. Our applications expertise covers a wide range of technologies such as capillary electrophoresis, real-time PCR, Pyrosequencing, and next-generation sequencing. Some of the products we have played a role in are shown below.

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Technology Knowledge

Bead-Mill Disruption

Rotor-Stator Disruption

Magnetic Bead Extraction

Spin-Column Extraction

Single Cell Isolation

Spectrophotometry

Large-scale sample disruption

Analysis of nucleic acids and proteins from biological samples are often a crucial part of medical and biochemical applications. Therefore, a fast and efficient method is needed for releasing these biomolecules from biological samples. Usually mechanical, physical, chemical and/or enzymatic methods are used to disrupt the biological matrixes and cells. In medium- to high-throughput workflows, bead-mill technology has proven to be an efficient method for disruption and homogenization of tissue samples and other biological materials. The mechanical disruption is the result of high-speed shaking of samples mixed with stainless steel, tungsten, carbide or glass beads, thereby beating and grinding the samples until they are sufficiently disrupted. This method is often combined with enzymatic lysis and/or physical disruption using liquid nitrogen for more efficient disruption and homogenization.

Fast release of biomolecules

A variety of fresh and frozen sample types are suitable for bead-mill disruption, including plant material and animal tissues. Some sample types, such as plant material, may require a pre-treatment in liquid nitrogen in order to properly release the biomolecules. Proper disruption leads to complete disruption of cell walls and membranes, while homogenization takes it further, shearing high-molecular-weight cellular proteins and carbohydrates. To ensure high yields, it is crucial that both the speed and the duration of the disruption/homogenization process are sufficient. A complete homogenization results in a homogeneous lysate, which subsequently can be used to give high yields of nucleic acids or proteins of interest in downstream purification protocols, thereby providing necessary material for downstream genomics, transcriptomics and proteomics applications.

For information about products based on this technology, see TissueLyser LT and TissueLyser II.

Rotor-Stator Disruption

Small-scale sample disruption

Analysis of nucleic acids and proteins from biological samples are often a crucial part of medical and biochemical applications. Therefore, a fast and efficient method is needed for releasing these biomolecules from biological samples. Usually mechanical, physical, chemical and/or enzymatic methods are used to disrupt the biological matrixes and cells. In low-throughput workflows, rotor-stator disruption is a suitable mechanical method. It’s carried out using a rotor-stator homogenizer, essentially a handheld high-speed blender, which mechanically shears the samples. The shearing is a result of both: the rotation of the blade and the turbulence in the sample. This method is often combined with enzymatic lysis and/or physical disruption using liquid nitrogen for more efficient disruption and homogenization.

Fast release of biomolecules

A variety of fresh and frozen sample types are suitable for rotor-stator disruption, including plant material and animal tissues. Some sample types, such as plant material, may require a pre-treatment in liquid nitrogen in order to properly release the biomolecules. Proper disruption leads to complete disruption of cell walls and membranes, while homogenization takes it further, shearing high-molecular-weight cellular proteins and carbohydrates. To ensure high yields, it is crucial that both the speed and the duration of the disruption/homogenization process are sufficient. A complete homogenization results in a homogeneous lysate, which subsequently can be used to give high yields of nucleic acids or proteins of interest in downstream purification protocols, thereby providing necessary material for downstream genomics, transcriptomics and proteomics applications.

For information about a product based on this technology, see TissueRuptor II.

Magnetic Bead Extraction

Fast and easy purification

A commonly used approach for nucleic acid extraction is based on magnetic bead technology. The sample containing the nucleic acids is mixed with a solid phase consisting of silica-coated magnetic beads. Since the nucleic acids will bind to the beads, they can easily be separated from the remaining solution thanks to their magnetic properties. After the separation, the beads are first washed before the nucleic acids are released from the beads by immersing them into elution solution.

A wide range of starting materials

Magnetic bead technology allows extraction and purification of eukaryotic, bacterial as well as viral DNA and RNA from a wide range of biological materials such as blood, tissues, as well as other type of materials like bacteria, viruses and plants. The purified nucleic acids can be used in downstream applications in biomedical research, molecular diagnostics and gene expression analyses.

For information about a product based on this technology, see EZ1 Advanced XL and QIAsymphony SP.

Spin-Column Extraction

Fast and efficient purification

Extraction and purification of RNA, DNA and proteins has been made exceptionally easy since the introduction of the silica-based spin columns in the 1980s. Spin-column extraction is a solid phase extraction method, which utilizes the fact that the target molecules bind to immobilized silica in the column. The cells are first lysed in lysis buffer and the lysate is allowed to bind to the silica in the spin-column. In order to force the solutions through the solid phase, the column is put in a benchtop centrifuge. The washing steps, including centrifugation, remove all impurities. The molecules of interest are finally eluted with an appropriate solution and centrifugation. The type of starting material and solutions used in the protocol will dictate the contents of the eluate.

A wide range of starting materials

Spin-column-based protocols for the extraction and purification of DNA, RNA or proteins have been developed for a wide range of biological materials such as blood, tissues, as well as other type of materials like bacteria, viruses, and plants. The purified biomolecules can be used in downstream applications in biomedical research, molecular diagnostics and gene expression analyses.

For information about products based on this technology, see QIAcube.

Singe-Cell Isolation

Individual and viable cells

Single cell isolation is a prerequisite for a number of medical and biochemical applications, such as RT-qPCR, genotyping, cellular phenotype determination, NGS (RNA sequencing and whole genome sequencing), protein analysis with labeled antibodies and genotyping. For these applications, it is crucial that truly individual cells have been isolated and that these cells are viable. In large scale-studies, it’s also essential to avoid labor-intensive methods. Therefore, various methods and devices, that increase the efficiency of single cell isolation have been developed.

Magnetic technology

One time-saving approach is based on magnetic technology. Here, the cells are cultivated on arrays packed with thousands of magnetic microrafts, where each raft is designed to hold single cells. The cells of interest are identified using a microscope, and the corresponding microrafts are dislodged from the array using a magnetic wand and finally transferred to a test tube or a cell culture dish. This method ensures minimal manipulation of the cells and cell viability for several days, thereby providing a good option for a wide range of downstream applications.

For information about products based on this technology, see QIAscout.

Spectrophotometry

Measuring quantity and quality

Accurate measurement and reliable quality control of DNA, RNA and protein samples is a prerequisite for a multitude of assays in medical research and biochemical applications. By using a spectrophotometer to read the UV/VIS absorption spectrum of a compound in a given sample, it is possible to measure the signal and calculate its quantity. Spectral profiling, i.e. reading the absorption of a sample at a range of different wavelengths, can reveal further information about the quality and the composition of the sample, e.g. detecting impurities. The profiles of different sample types are unique; e.g. a pure RNA sample will give rise to a profile that is decidedly different from an RNA sample spiked with gDNA.

Reproducibility and linearity

In order to ensure that the measurements are reliable, serial dilutions of the samples should be made to calculate the linearity. The regression coefficient should optimally be >0.999, but this is difficult to achieve with manual measurements. Therefore it’s useful to employ automated spectrophotometry systems, providing the high system linearity and reproducibility required for many molecular biology applications.

For information about products based on this technology, see QIAxpert.

Capillary Electrophoresis

Liquid Handling

Automated Sealing

Real-Time PCR

Pyrosequencing

Next-generation Sequencing

High resolution separation of biomolecules

Capillary electrophoresis is a method that utilizes narrow capillaries (typically made of silica) under high voltage for the separation of ions, molecules or molecular complexes. In many applications, it can replace traditional slab-gel electrophoresis of nucleic acids and proteins. It can be performed with or without a gel, or with a special polymer solution inside the capillaries, either under native or denaturing conditions. Modern instruments allow full control of all electrophoretic parameters and thus provide high reproducibility, which often is associated with high resolution; thus, in DNA analyses it is often possible to achieve 1 bp resolution. The diameter of the capillaries is generally between 20 and 100 μm and the length 17–100 cm, so that the capillary volume typically is 10–100 μl. The inner wall of the capillaries may be coated to control both the interaction of the analytes with the silica surface and the electroendoosmotic flow. The outer capillary surface is polymer-coated to improve its mechanical stability.

Samples can be loaded into the capillaries either by electrokinetic injection (applying a high voltage for a short, defined period of time) or by hydrostatic pressure. Another difference, in comparison to gel electrophoresis, is that in capillary electrophoresis a detector remains fixed, so that all of the analytes must travel the same distance. The migration time is then used to identify each analyte in every sample. In addition, many samples may be run simultaneously, each sample in its own capillary. The results are usually displayed as electropherograms. The analytes can be detected using a number of detection methods, including UV absorbance, fluorescence, refractive index, etc. Using appropriate standards, the peak area in each electropherogram can be correlated with the amount of each analyte, and thereby its concentration can be determined.

Capillary electrophoresis has many advantages compared to slab gel electrophoresis and HPLC; it gives high efficiency separations, it’s automated, affordable and environment-friendly. In addition, it only requires small sample volumes, it’s fast and easy to perform. Since the sensitivity that can be achieved by capillary electrophoresis is extremely high, the method also allows analysis of samples containing very low analyte concentrations. Different modes of CE, as for example capillary zone electrophoresis, capillary gel electrophoresis, capillary isoelectric focusing and affinity CE, microfluidic CE, provide a large choice of operating modes from which one can select the best suited for a particular analytical application.

Downstream applications

Being a versatile, fast and accurate separation method, capillary electrophoresis can ideally be used for protein and nucleic acid analysis in a number of different applications, involving sequencing, size analyses and quality control. Apart from using it for direct analysis of PCR/RT-PCR amplicons, restriction fragments, cDNA and NGS libraries, it can also be advantageous to include it in workflows involving genotyping, CRISPR, gene expression and regulation, and next-generation sequencing.

For information about a product based on this technology, see QIAxcel Advanced.

Liquid Handling

Automation for accuracy

The increasing demand for reliable high-throughput protocols in medical research and life science applications has created a growing market of automated liquid handling systems. They provide the required accuracy and reproducibility for state-of-the-art PCR, NGS technologies as well as sample preparation for the other downstream processes. Moreover, the automated systems are enabling large-scale studies and saving a lot of time for the laboratory personnel.

Reproducible pipetting

Automated pipetting systems are robotic instruments used to dispense predefined volumes of reagents and samples into vessels such as test tubes or 96-well plates in order to avoid manual intervention thereby ensuring consistent accuracy and reproducibility. These instruments feature robotic hands which handle single or multi-channel pipettes matching tip arrays. Instruments that utilize liquid displacement pipetting technology offer the choice between fixed and disposable tips and a wide range of pipetting volumes. Air displacement technology on the other hand eliminates the need for daily maintenance, since system liquids aren’t required. Today, there are automated pipetting systems offering both of these technologies. The advanced designs of the automated pipetting systems offer safe and reliable pipetting while preventing contamination and carry-over simultaneously that is a prerequisite for most downstream molecular biology applications today.

For information about products based on this technology, see QIAgility, QIAsymphony AS

Automated Sealing

Bead sealing for reproducible qPCR

Maintaining the integrity of qPCR samples is essential, but sometimes difficult to achieve with the designs of qPCR vessels and plate sealing available on the market today. The use of individual tube caps, cap strips or tapes renders a high risk of incomplete sealing of the sample tubes, likely leading to evaporation and contamination of the samples. Hence, a technology which helps eliminating these risks is of great interest. To accommodate this issue, an automated module for dispensing beads into qPCR sample tubes and 96-well plates has been developed. It holds a proprietary bead dispenser (adaptable for a variety of bead diameters), which dispenses beads into each chosen vessel and seals them by a controlled force via a plunger that presses the beads into a vessel, thereby securing maximal tightness. The bead dispenser holds up to 360 pieces of 4 mm diameter beads, which are dispensed at a 100 % dispensation rate, and thus contribute substantially to the high reliability of this module.

Safety and flexibility

The bead sealing device has been designed for maintaining an absolute integrity of the samples. To prevent any degradation of the samples a cooling plate can be positioned below the sample plate. The vessels are efficiently sealed by the beads and an integrated optical sensor can perform a load-check of the beads if needed. The safety of the qPCR system is further ensured with the actual design of the bead sealing module that inherently prevents any cross-contamination. Thereby, the Bead Sealer provides an attractive combination of safety features while simultaneously ensuring a minimum of hands-on tasks. The only manual intervention required is supplying the samples and selecting a suitable program to define the vessels or plates that need to be sealed. It is compatible with different interfaces so that the data can be transferred via cloud, WLAN or Bluetooth. Due to its flexibility and safety features, the bead dispenser can therefore easily be integrated in any existing workflow. The bead sealing module hence provides a good option for improving the efficiency and reproducibility of high-throughput qPCR workflows.

For information about products based on this technology, see TubeSealer.

Real-Time PCR

Monitoring DNA amplification

Real-time polymerase chain reaction (RT-PCR), also known as quantitative PCR, provides an elegant solution for quantification of DNA sequences in real time, as opposed to conventional PCR, where only the final result of the PCR amplification can be analyzed. The amplification reaction progresses due to repeated cycles of heating and cooling at predefined temperatures for every stage, which are referred to as denaturation, annealing and elongation. The PCR also requires specific reagents, namely DNA template, DNA polymerase, primers (oligonucleotides) serving as starting points and thereby guiding the amplification, as well as dNTPs, serving as building blocks. In order to follow the amplification process in real-time, fluorescent dyes are linked to the primers so that the DNA amplification can be traced; i.e. the fluorescent signals are effectively reporting snapshots of the reaction to the software. The reaction can either be traced with one dye only, e.g. SYBR® Green, or with up to 6 dyes for multiplex RT-PCRs where several DNA targets are amplified simultaneously. This requires a RT-PCR cycler with 6 optical channels, as in the Rotor-Gene Q. Throughout the amplification process, the RT-PCR cycler will send optical data to its software, which will display the results as a curve indicating the amount of signal, i.e. the amount of amplification, in each cycle.

Sensitivity and accuracy

Successful RT-PCR runs rely on high-precision technology; they require a reliable RT-PCR cycler with minimal tube-to-tube variation, fast ramp rate, and optical and thermal accuracy. Different solutions can be used to reach a precise and uniform temperature across all samples in a short period of time during the reaction; for example, Peltier elements and air flow or liquid flow are efficient in controlling and evening out the temperature. The excitation of the fluorescent dyes can be achieved by light sources, such as a halogen, UV, LED lights or a Xenon lamp in combination with dye-specific filters. The signals are captured by a detector (e.g. a photodiode or a CCD), amplified by the photomultiplier and sent to the software.

Downstream applications

Over the years, the technology mentioned above has enabled RT-PCR cyclers to become increasingly sophisticated and reliable, and hence today RT-PCR plays an essential role in many biomedical applications such as gene expression analysis, pathogen detection, DNA methylation analysis, SNP genotyping and gene scanning, as well as miRNA research.

For information about products based on this technology, see Rotor-Gene Q.

Pyrosequencing

Shedding light on DNA sequences

Pyrosequencing is a high-throughput sequencing-by-synthesis method used to quantify sequence variation. It’s based on a chemical reaction that generates a sequence of light signals, which reflects the sequence of the nascent DNA.

Efficient chemistry

The pyrosequencing reaction relies on the action of four enzymes: DNA polymerase, ATP sulfurylase, luciferase and apyrase. DNA polymerase is used to elongate the DNA, upon which pyrophosphate is released. ATP sulfurylase converts the pyrophosphate to ATP, which is used by the luciferase to oxidize luciferin to oxyluciferin. This reaction generates a light signal, which is detected by a camera and displayed as peaks in a so called pyrogram. At the end of each reaction cycle, apyrase removes any unincorporated nucleotides left in the reaction.

The amount of light released in each pyrosequencing reaction, i.e. the height of each peak, is directly proportional to the number of incorporated nucleotides. If for example 3 nucleotides are incorporated, three ATPs are generated giving rise to triple peak in the pyrogram. The DNA sequence can be determined since the four nucleotides A, C, G and T are dispensed in a predefined order, so that each signal peak can be correlated with a specific nucleotide. This sequencing technology provides quantitative real-time data that can be used for characterization of single nucleotide polymorphisms (SNPs) and insertions-deletions (indels), as well as quantification of allele frequencies and DNA methylation levels.

For information about products based on this technology, see PyroMark.

Next-generation Sequencing

From single DNA sequences to massively parallel sequencing

After over 20 years of conventional Sanger sequencing, next-generation sequencing (NGS) emerged in 2004. With this high-throughput technology, the efficiency of sequencing increased with a significant leap. Rather than merely sequencing single DNA sequences, it was now possible to perform parallel sequencing of many short DNA fragments so that e.g. the whole human genome could be sequenced in less than a week at a fraction of the cost.

Sequencing technologies

Under the NGS label, we can include the so called second, third and fourth generation sequencers. Nowadays, there are several technologies utilizing a variety of methods, as for example:

Illumina — sequencing by synthesis (bridge amplification) and detection of fluorescence signals
Ion Torrent — sequencing by synthesis (emulsion amplification) and detection of changes of pH by an ion semiconductor
Pacific Biosciences — single-molecule real-time sequencer
454 Life Sciences — sequencing by synthesis (emulsion amplification) and detection of pyrosequencing signals
SOLiD — sequencing by ligation (emulsion amplification) and detection of fluorescence signals
Qiagen GeneReader — sequencing by synthesis (emulsion amplification) and detection of fluorescence signals
Oxford Nanopore — Nanopore DNA sequencing

Sequencing workflow

NGS workflow is a complex process which involves several steps. A typical workflow includes:

Nucleic acid extraction
Fragmentation and quality control (QC)
Target enrichment (optional) and QC
Library preparation and QC
Clonal amplification (optional)
Sequencing
Data analysis and interpretation

NGS is used for different applications, such as whole genome and whole exome sequencing, transcriptome profiling, targeted DNA re-sequencing, epigenomics, etc.

NGS workflow key points

Nucleic acid extraction

The origin of the biological material to be studied influences both the amount and the quality of the extracted nucleic acids; i.e. the DNA or RNA can be degraded/compromised to varying degrees. Also, the heterogeneity of the starting material dictates the most suitable workflow to be used for the purpose of the study (e.g. whole genome versus target re-sequencing, sequencing technology and secondary analysis algorithms).

Target enrichment

Depending on the mutations or variants to be investigated, the target enrichment can either be hybridization-based or multiplex PCR-based or simply not implemented at all if whole genome sequencing is required. A target enrichment step normally increases the NGS turnaround time, but on the other hand it allows the analysis to focus more on the genetic traits that really matter. In this way, it is possible to optimize the output of the subsequent NGS platform by allowing higher multiplexing.

Sequencing

In the next step, target libraries or single nucleic acids are subjected to sequencing. For the most common second generation NGS sequencers, the templates are subsequently subjected to reagents containing DNA polymerase and labeled or native dNTPs. Labeled nucleotides generally contain a fluorescent dye, which is different for each base (A, C, G and T). The DNA polymerase incorporates the dNTPs to the ends of the growing DNA strands, which will give rise to patterns of fluorescent signals or released protons reflecting the composition of each DNA sequence of the libraries. The released protons or fluorescent signals are subsequently detected by sensors or high-resolution digital cameras, respectively. The signals are then registered and analyzed by the corresponding NGS sequencer software and the DNA sequences are finally digitalized and compiled in the form of *.fastq files suitable for downstream bioinformatics software analyses.

Library preparation

Library preparation is a multistep procedure, which is specific for each platform. The aim of this step is to ligate sequencer-specific adapters and to distinguish the samples from one another using barcodes; thereby, the sequencer can process more than one sample at a time. Fourth generation sequencers don’t require library preparation, as the templates don’t need to be mobilized on a solid substrate, but on the other hand they don’t allow multiplexing of samples in a single run.

Clonal amplification

For second generation NGS technologies (e.g. the Qiagen GeneReader platform), the last step before sequencing is a so called clonal amplification. Sequencing libraries are immobilized on a solid substrate (flow cell or beads) and clonally amplified to allow signal detection during sequencing. Clonally amplified targets are then hybridized with sequencing primers to allow base incorporation during the sequencing step. This step isn’t required for third (e.g. PacBio) and fourth (Oxford Nanopore) generation NGS technologies, which perform single nucleic acid sequencing.

Data analysis and interpretation

The final results (i.e. *.fastq files) are further processed by dedicated bioinformatic pipelines, which present the change in the genomic sequence of each biological sample and compares it to a given reference sequence. Alternatively, the data can be used to build up a new reference sequence. When studying genomic mutations, the observed variations may eventually be associated with pathogenic variations, such as somatic variations detected in cancer cells, germline mutations associated with inherited diseases and other genetically associated diseases.

For information about an NGS workflow based on this technology, see Qiagen GeneReader NGS.

Reference Products

TissueRuptor II

TissueLyser LT

TissueLyser II

QIAcube

QIAcube HT

QIAsymphony SP

Low-throughput sample disruption

The TissueRuptur II is a hand-held homogenizer with a rotating blade used to rapidly disrupt a range of fresh or frozen biological sample types in order to enable purification of RNA, DNA and proteins. Most sample types can be thoroughly processed within a minute. Although only one sample can be handled at a time, the fact that the probe is disposable ensures the user to process a large number of samples within a short time without compromising on sample quality.

Speed and safety

A typical run takes 15–120 seconds, and the rotating blade operates within a variable speed range of 5,000–35,000 rpm. The sample is simply submerged in lysis buffer (animal tissues) or liquid nitrogen (plant material), and disruption at full speed for approximately 30 seconds is usually sufficient for complete homogenization of the sample. The TissueRuptur II is provided with disposable probes, thus eliminating the risk of cross-contamination. Furthermore, the probes are transparent, which means that the disruption process easily can be monitored visually thereby ensuring a complete homogenization. Efficient disruption of the samples is a prerequisite for efficient nucleic acid and protein purification.

Multiple downstream applications

The TissueRuptur is intended for molecular biology applications relying on thorough and rapid disruption of biological samples. Efficient homogenization ensures that the samples can give high yields of DNA, RNA and proteins to be used in genotyping, gene expression studies or proteomics. The simplicity of the disruption process means that it can seamlessly be integrated in any pre-existing sample purification workflows. Published results based on the use of TissueRuptur and sample preparation kits demonstrate that the TissueRuptur ensures efficient disruption and homogenization of animal tissues, successful purification of phosphoproteins, high performance results in PCR, as well as reproducible purification of high-quality genomic DNA.

Low- to medium-throughput sample disruption

The TissueLyser LT is designed for low-to medium throughput disruption of human, animal and plant tissues as well as bacteria and yeast samples. The process is based on bead mill technology, with high-speed shaking in plastic tubes with stainless steel or glass beads which are 5 mm or 7 mm in diameter. Bead Dispensers are provided to ensure that the correct amount of beads is dispensed into the samples. Up to 12 samples can be processed simultaneously and a cooled adapter prevents degradation of the biomolecules.

Efficient processing

The release of nucleic acids from the sample material relies on proper disruption followed by homogenization of the starting material. TissueLyser LT performs both, disrupts and homogenizes the material, making sure that carbohydrates also are sheared, as opposed to a mortar and a pestle, which only disrupt the material. Thorough shearing of carbohydrates is a prerequisite for efficient purification of nucleic acids in downstream applications. The sample homogenization is achieved by running the TissueLyser LT at variable speeds from 15 to 50 Hz (900–3000 oscillations/minute) and the run times ranges between 1 second and 1 hour 59 minutes.

Quality and versatility

The TissueLyser LT is suitable for disruption and homogenization of a wide range of biological starting materials. Even samples that are normally difficult to lyse, such as heart and brain tissues can be successfully processed using the TissueLyser LT, ensuring that the released DNA, RNA and proteins remain intact. The high performance of the instrument in combination with its compact design, the coolable adapter and its compatibility with all laboratory workflows renders it a useful tool for any small-scale molecular biology applications that require rapid homogenization of samples, as wells as high sample quality.

Medium- to high-throughput sample disruption

The TissueLyser II is designed for medium- to high- throughput disruption of human, animal and plant tissues as well as bacteria and yeast samples. The process is based on bead mill technology, with high-speed shaking in plastic tubes with stainless steel, tungsten, carbide or glass beads, which are 3 mm, 5 mm or 7 mm in diameter. Bead Dispensers are provided to ensure that the correct amount of beads is dispensed into the samples. The tissues can also be processed with grinding jar sets made of Teflon or steel. Up to 48 or 192 samples can be processed simultaneously, and the provided adapter sets ensure the disruption optimal for the chosen quantity.

Efficient processing

The release of nucleic acids from the sample material relies on proper disruption followed by homogenization of the starting material. TissueLyser II performs both, disrupts and homogenizes the material, making sure that high-molecular-weight cellular proteins and carbohydrates are also sheared, as opposed to a mortar and a pestle, which only disrupt the material. Thorough shearing of these molecules is a prerequisite for efficient purification of nucleic acids in downstream applications. The sample homogenization is achieved by running the TissueLyser II at variable speeds from 3 to 30 Hz (180–1800 oscillations/minute) and the run times range between 10 seconds and 99 minutes.

The TissueLyser II is suitable for convenient and secure disruption and homogenization of a wide range of biological starting materials. Even samples that are normally difficult to lyse, such as heart and brain tissues can be successfully processed using the TissueLyser II, ensuring that the released DNA, RNA and proteins remain intact. The high performance of the instrument renders it a useful tool in any large-scale molecular biology applications that require rapid homogenization of samples, as wells as high sample quality.

Case Study QIAcube

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The Challenge

The majority of nucleic samples preps are done manually by the scientist at low throughput with 1-12 samples at a time. Can we help scientist to automate their sample prep tasks and free up their time for more important scientific work?

The Goal

Automate the manual nucleic acid purification process, while leaving the manual purification chemistry and protocols unchanged. The scientist would not have to re-validate their workflows and the hurdle to switch. Keep the sales price for the system below the investment barrier at the average Universities and Research Institutions. The hurdle to switch to an automated method is minimal.

The Approach

Identify appropriate automation technology to process manual spin columns; positive pressure, vacuum, centrifugation. Automated centrifuge with integrated consumable handling Sophisticated disposable centrifuge cartridge for sample processing and liquid waste handling. Establish a corporate instrument design and branding. Design to cost for higher volume production.

The Result

Many thousand units have been installed. QIAcube has become the reference automated low throughput nucleic acid purification and is still unrivaled in its market.

Mid- to high-throughput nucleic acid purification

QIAcube HT performs mid- to high-throughput automated purification of nucleic acids in a 96-well format. The instrument is based on silica membrane technology and thus yields high quality nucleic acids intended to be used for molecular biology applications.

Safe and standardized

The QIAcube HT can be used for purification of a wide range of compounds such as DNA, RNA and miRNA from virtually all sample types, including cells, tissues, stool samples, raw or processed food material as well as bacteria and viruses. In order to keep a safe environment within the instrument, a HEPA filter is used to purify the air and maintain a positive air pressure while the UV light decontaminates the worktable and prevents cross-contamination. There is also a tip ejection feature, making sure that used tips are collected externally thereby keeping the internal workspace clean, as well as dedicated plasticware ensuring reliability and convenience.

Simple integration in workflows

The straight-forward purification procedure can seamlessly be integrated in a number other workflows. The eluted nucleic acids samples are collected in tubes that are compatible with downstream applications carried out in QIAgility and different detection systems. Purification steps can easily be included into more complex workflows. The simplicity of the procedure is also enhanced by its intuitive software, where the graphical user interface simulates the instrument worktable and allows a run to be initiated with only a few mouse clicks. The data from each run as well as bar codes and other specific information is easy to manage and can readily be integrated in the Laboratory Information Managements Systems (LIMS). The combination of being a high quality, high-throughput bench-top instrument and having a noticeably compact design, makes it a valuable option for biosafety level laboratories.

Case Study QIAsymphony

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The Challenge

Decentralized molecular testing by enabling medium throughput laboratories. Molecular testing is largely centralized in specialized laboratories, reference labs and large hospitals. Sample types are very diverse, come in very different containers and need to be tested for a broad range of diseases.

The Goal

Build a system that accommodates for the immense variety of setups of medium throughput testing labs. All samples types and input formats will be accepted by the system. 1 to 96 samples, input volumes from 100 ul to 1 ml and processing of any type of PCR assay gives the operator highest flexibility. Despite its flexibility, the system will be set up in less than 15 min. and run from start to finish without user intervention.

The Approach

In order to accommodate the various setups and demands of the laboratories a modular system design with sample preparation, assay setup and analysis was chosen. Ease of use and quick setup of the system was achieved with a disposable, pre-filled reagent cartridge design loaded into an easily accessible drawer. The sample input and output area can be loaded with individual tubes or microplates. The system is operated via touchscreen. The core sample processing module can be extended with either an assay setup module or an automated PCR cycler unit for up to 140 analyses per run.

The Result

2000 units have been sold globally so far. QIAsymphony is the undisputed standard in automated nucleic acid sample processing for the medium throughput laboratory.

Case Study QIAsymphony Cartridge

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The Challenge

Biological samples are extremely divers requiring a large number of methods and chemistries to purify nucleic acids and provide them in a format for further processing.

The Goal

Build a low cost disposable, pre-filled, IVD compliant cartridge that accommodates dozens of different magnetic bead chemistries. The cartridge is filled, assembled and sealed in an automated production. Will be opened automatically by the QIAsymphony system and can be resealed if not completely used. The shelf life of the cartridge is > 1 year. Productions cost are equal to or lower than comparable spin column products.

The Approach

Individual troughs are deep-drawn and heat sealed for low cost and long-term storage. The heat seal withstands aggressive chemicals for an indefinite storage period. Troughs are held together with a frame for easy handling. A 2D barcode will identify the individual troughs. A plastic disposable piercing device is used to punch holes to allow the pipetting head to pick up reagents. Low volume enzymes are stored in a separate rack for cold storage and can be attached to the through rack to build one handling unit.

The Result

The QIAsymphony cartridge is an extremely cost-effective and reliable reagent storage container used thousand-fold in diagnostic laboratories around the world.

EZ1 Advanced XL

QIAscout

QIAxpert

QIAgility

TubeSealer Module

QIAsymphony AS

Automated nucleic acid purification

The EZ1 Advanced XL is a desktop instrument designed to perform automated isolation and purification of nucleic acids, such as eukaryotic DNA, mRNA, total RNA as well as viral RNA and DNA. The system is based on proven magnetic bead technology and can process up to 14 samples in each run in 20 minutes. The process consists of reading the reagent and sample information with a bar code scanner, lysing the samples, binding the nucleic acids to the beads, washing and finally eluting the nucleic acids.

Safety and accuracy

The integrity of the samples and the reproducibility of the procedures are ensured by the design of the instrument. A UV light is used for decontamination, efficiently eliminating any Gram-positive and Gram-negative bacteria inside the instrument. In addition, a sensor makes sure the instrument door is closed during sample preparation, thereby further protecting sample integrity. Manual intervention is kept to a minimum by providing EZ 1 Kits containing all necessary reagents in a format that can be processed automatically by the instrument, from the opening of reagent cartridges to the elution of nucleic acids. Furthermore, the instrument contains high-precision syringe pumps with tip adapters holding filter tips, which can aspirate and dispense 50–1000 µl liquid with exceptionally high accuracy.

Traceability and versatililty

Samples and consumables can easily be tracked using the bar code reader and the manual keyboard. All system parameters and run data are stored in the system and are readily accessible. The instrument will generate a pdf and a csv result file after each run. The report files can either be exported to a LIMS (Laboratory Information Management System) or other programs for any downstream applications. The provided EZ1 Kits are available for a large number of applications used in forensics, biomedical research, molecular diagnostics and gene expression analysis.

Efficient single-cell isolation

The QIAscout is a device based on magnetic technology and is used to efficiently isolate and recover single cells. The isolation can be carried out within minutes and the method ensures minimal manipulation of the recovered cells. After the isolation, the isolated cells can be used for direct analysis or clonal expansion. The procedure only requires a cell sample, QIAscout and an inverted microscope. The device comes with an array coated with magnetic nanoparticles and packed with 12,000 microrafts, which serve as releasable culture sites for individual cells or clones. The system also includes a release device, a magnetic wand and a magnetic collection plate.

Simple and straight-forward

The workflow is exceptionally easy. Initially, the cells have to be seeded and cultivated on the QIAscout array. The release device with its release needle is then placed on the microscope objective, while the array is placed on the microscope stage. As soon as the cells of interest have been identified, the corresponding microrafts are pierced, dislodged and transferred to vessels, e.g. reaction tubes or cell culture dishes, using a magnetic wand. Since the cell viability and purity is maintained, as proven by several studies, the collected cells can be used for several applications.

Multiple applications

The QIAscout is intended for molecular biology applications, including single-cell sequencing, whole genome and transcriptome amplification and single-cell miRNA analysis, as well as generation of clonal subpopulations. QIAscout can be used for a variety of eukaryotic cell types and the selection of cells can be based on morphology, fluorescence or other parameters, making it even easier to integrate the method into existing workflows. Moreover, the cells are viable for several days after the selection, giving the user more flexibility in designing the workflow.

Fast check of nucleic acids

QIAxpert is a microfluidic UV/VIS spectrophotometer used to discriminate between DNA and RNA and sample impurities by using unique spectral profiling protocols. The instrument can easily quantify up to 16 samples of nucleic acids within 2 minutes and highly accurate readings can be made from just 2 µl of sample. Nucleic acid quantification and quality control can be performed by simply pipetting the samples on a microfluidic slide, placing it into the reader and selecting the method on the intuitive, integrated touchscreen. Thanks to the capillary channels in the slides, evaporation is prevented so that the samples can be preserved for up to 2 hours.

High reproducibility

Serial dilutions of samples from gDNA have proven that the quantifications measured by the system are in high concordance with the actual concentrations thus yielding accurate and reliable quantifications. Furthermore, repeated quantification across the complete dynamic range of concentrations of dsDNA samples has proven the measurements to be highly reproducible, having minimal standard deviations and thus low variability between the samples.

Intuitive software

Since QIAxpert features an integrated touchscreen, so that no additional hardware is needed. The QIAxpert Software is designed to be fast and easy to use and can selectively quantify DNA, RNA and proteins in the samples. The specific amounts of DNA, RNA and contaminant in the samples can swiftly be determined by the intelligent software algorithms and comprehensive reports can be viewed directly on the integrated screen or exported to a USB stick and viewed on a computer or even a smart device by scanning a QR code. The report options are flexible, so that either html, CSV or txt formats can be selected for viewing the data. QIAxpert thereby offers a unique combination of features for fast and flexible nucleic acid quality control and quantification.

High-precision automated PCR setup

The QIAgility is a compact benchtop workstation used to automatically set up PCR assays with exceptionally high-precision. Since all manual pipetting steps are eliminated, QIAgility can ensure both reproducibility and increased productivity. It features a single channel pipetting head, delivering fast and safe transfer of liquids, and features dynamic liquid-level sensing with a minimum detection volume of 10 µl.

Pure pipetting accuracy

The reproducible and highly accurate PCR setup mainly relies on the exceptionally high quality of the dispensations, which range between 1 µl and 200 µl. This is enabled by the QIAgility Setup Manager software and the precision of the dispensed volumes has been verified by repeated tests in various settings. The high sensitivity of the system is ensured by its ability to sense the meniscus during pipetting and retracting the tip during dispensation, thereby increasing the accuracy and minimizing any carry-over. If the liquids are viscous, the pipetting speed will be adapted accordingly. Tests with serial dilutions have proven that the linearity of system is exceptional, with a regression coefficient of >0.999. Moreover, the software provides step-by-step guidance and automatically calculates all mixes, so that no pipetting steps need to be programmed. Any contamination of the samples is prevented by an optional UV light and the HEPA filter system ensures positive pressure of clean air within the instrument. In addition, all used tips are ejected externally, so that no waste is accumulated on the worktable.

Flexibility and applications

The PCR assay setup performed by QIAgility can easily be integrated into various workflows. Almost all tube and plate formats are supported, such as 96-well and 384-well plates, but also Rotor-Discs for the Rotor-Gene® Q real-time PCR instrument. For added convenience, a laptop computer with intuitive software is provided. The user can program various pipetting applications, such as normalization of DNA and RNA concentration, transfer of liquid samples between different tube formats, serial dilutions with variable dilution ratios, restriction digest setups, sample pooling and selective pipetting from archived sample banks.

TubeSealer module enables automated qPCR tube sealing

The TubeSealer is a module that performs fully automated sealing of qPCR reaction vessels. It consists of a proprietary bead dispenser (1,2) that dispenses beads into each selected vessel using a plunger. The plunger applies a defined force to the beads to achieve maximal tightness.

Pure reliability

The bead dispenser holds up to 360 beads of 4 mm diameter, which are dispensed at a 100% dispensation rate securing high reliability. A plunger presses the beads into each vessel, efficiently sealing them for the subsequent qPCR. The design of the instrument inherently prevents any cross-contamination between the samples. To further increase the safety of the process, the tightness of the seal is checked and confirmed by a built-in optical sensor. To prevent any degradation of the samples, a cooling plate can be positioned below the sample plate. The only manual intervention required for the process is supplying the samples and selecting a suitable program. As an option, a load-check of the vessels can be performed if necessary. All these features combined, ensure that the integrity of the samples is maintained throughout the PCR process.

Exceptional flexibility

The TubeSealer is incredibly flexible when it comes to throughput, vessel type, vessel dimensions, liquid volume and communication interface. The instrument can be used equally well for any throughput; low, medium or high. It is compatible with a wide range of tube sizes and designs, such as single tubes, tube strips, 96-well plates, discs, conveyor belts, etc. The bead dispenser can be adapted to different bead sizes required for various diameters of the tubes. The instrument is also compatible with different interfaces, so that data can be transferred via cloud, WLAN and bluetooth. The instrument is designed in the way that is possible to seamlessly integrate instrument software compliant with the SiLA standard for software control. These properties truly demonstrate the flexibility of the automated sealing process carried out by the TubeSealer module.

TubeSealer MORE DETAILS

Case Study QIAsymphony

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The Challenge

Decentralized molecular testing by enabling medium throughput laboratories. Molecular testing is largely centralized in specialized laboratories, reference labs and large hospitals. Sample types are very divers, come in very different containers and need to be tested for a broad range of diseases.

The Goal

Build a system that accommodates for the immense variety of setups of medium throughput testing labs. All samples types and input formats will be accepted by the system. 1 to 96 samples, input volumes from 100 ul to 1 ml and processing of any type of PCR assay gives the operator highest flexibility. Despite its flexibility the system will be setup in less than 15 min. and run from start to finish without user intervention.

The Approach

In order to accommodate for the various setups and demands of the laboratories a modular system design with sample preparation, assay setup and analysis was chosen. Ease of use and quick setup of the system was achieved with a disposable, pre-filled reagent cartridge design loaded into an easily accessible drawer. The sample input and output area can be loaded with individual tubes or micro- plates. The system is operated via touchscreen. The core sample processing module can be extended with either an assay setup module or an automated PCR cycler unit for up to 140 analyses per run.

The Result

2000 units have been sold globally so far. QIAsymphony is the undisputed standard in automated nucleic acid sample processing for the medium throughput laboratory.

Case Study QIAsymphony Cartridge

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The Challenge

Biological samples are extremely divers requiring a large number of methods and chemistries to purify nucleic acids and provide them in a format for further processing.

The Goal

Build a low cost disposable, pre-filled, IVD compliant cartridge that accommodates for dozens of different magnetic bead chemistries. The cartridge is filled, assembled and sealed in an automated production. Will be opened automatically by the QIAsymphony system and can be resealed if not completely used. Shelf life of the cartridge is > 1 year. Productions cost are equal or lower than comparable spin column products.

The Approach

Individual troughs are deep-drawn and heat sealed for low cost and long term storage. The heat seal withstands aggressive chemicals for an indefinite storage period. Troughs are hold together with a frame for easy handling. A 2D barcode will identify the individual troughs. A plastic disposable piercing devise is used to punch holes to allow pipetting head to pick up reagents. Low volume enzymes are stored in a separate rack for cold storage and can be attached to the through rack to build one handling unit.

The Result

The QIAsymphony cartridge is an extremely cost-effective and reliable reagent storage container used thousand-fold in diagnostic loaboratories around the world.

Rotor-Gene Q

QIAxcel Advanced

PyroMark Platforms

GeneReader NGS

Rapid and reliable DNA and RNA analysis

The QIAxcel Advanced System is specifically designed for quick and accurate DNA and RNA analysis and thereby allows efficient and simple workflows. The instrument carries out sensitive high-resolution capillary electrophoresis of up to 96 samples per run in a few simple steps. The operator simply loads the gel cartridge, fills and loads the buffer tray, loads the samples and selects the process profile. Since it is an automated instrument, it is safe and suitable for high-throughput applications There is no need for gel preparation and the amount of hands-on work is minimized, thereby increasing the reproducibility and saving time and costs.

Software for easy quality control and quantification

QIAxcel ScreenGel Software is an interactive and user-friendly tool for data collection and analysis. The features can easily be customized and settings, such as run parameters, alignment and DNA size markers, can be adapted to the user’s applications. Furthermore, the software features RNA Integrity Score (RIS) which is used to measure the quality and integrity of the analyzed RNA samples. Since the measurement is objective, it’s a useful tool for quality control in all workflows that require RNA integrity, so that only high-quality samples are used throughout the workflows. Finally, the software also supports safe data handling, so that the data are password-protected and automatically saved and archived.

Wide range of applications

With its wide range of applications, the instrument is well suited for both academic and industrial laboratories. It can be preprogrammed to separate and analyze single or multiple PCR fragments, digested DNA, genomic DNA, synthesized oligonucleotides, total RNA and cRNA. Thereby, it can for example be used for bacterial genotyping, PCR fragment analysis, mutation detection, quality control of genomic DNA, detection of food allergens, pre-sequencing testing, NGS library QC as well as total RNA and cRNA for RT-PCR. The versatility, efficiency and reliability of the instrument make it an incredibly useful tool in any workflow including DNA and/or RNA analysis.

Quantifying sequence variations with pyrosequencing

The PyroMark platforms are used for rapid and accurate quantification of genetic and epigenetic DNA modifications using pyrosequencing assays. They can be used for advanced methylation, mutation and SNP quantification but also for verification and validation of samples from NGS and array experiments. The PyroMark platform consists of PyroMark Q24, PyroMark Q24 Advanced, PyroMark Q48 Autoprep, and PyroMark Q96 ID. PyroMark Q24 can analyze up to 24 samples in 15 minutes, can read up to 80 bp and performs mutation analysis and resistance typing. PyroMark Q24 Advanced shares those features but can read up to 140 bp and perform more complex mutation analyses, as well as epigenetic (CpG and CpN) analyses and microbial typing. PyroMark Q48 Autoprep with automated sample preparation is used for similar applications and can read equally long sequences, but can analyze up to 48 samples at a time. Finally, PyroMark Q96 ID has the capacity of analyzing up to 96 samples in each run.

From pyrosequencing to analysis reports

The pyrosequencing reaction relies on the release of light signals, where the amount of light is directly proportional to the number of incorporated nucleotides. The four nucleotides A, C, G and T are dispensed in a predefined order and as the DNA is elongated, pyrophosphate is released and converted to ATP, which is used by luciferase to generate light. The result of each dispensation of nucleotides is shown in the pyrogram, so if for example 3 nucleotides are incorporated (e.g. AAA), three ATPs are generated giving rise to triple peak in the pyrogram. If no nucleotides are incorporated, there is no light signal and thus no peak. The PyroMark software can be set up in different analysis modes in order to target analysis of for example SNPs, CpGs or perform base-calling of unknown sequences. When the analysis has been finalized, the software will generate comprehensive reports displaying the results as pyrograms as well as presenting statistics such as methylation percentage, allele frequencies and other analysis results.

Case Study GeneReader

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The Challenge

The capacity to sequence all 3.2 billion bases of the human genome has increased from 1.3 human genomes sequenced annually to 18,000 human genomes a year within a decade. Despite this improvement sequencing a genome is still an extremely complex procedure, which prevents its broad use in routine human diagnostics.

The Goal

Build a complete NGS workflow with seamlessly integrated automated components offering ease of use and efficiency from sample to result. Provide actionable insights with validated gene panels and fully integrated bioinformatics.

The Result

The GeneReader is the only integrated NGS workflow from sample to insight.

The Approach

The GeneReader workflow includes the following 6 processes: sequencing primer hybridization, flow cell preparation, reagents preparation, experiment set-up, flow cell loading and run start and post-run maintenance wash.

Precise and robust real-time PCR

The real-time PCR-cycler Rotor-Gene Q is designed to be used for real-time and end-point thermal cycling using polymerase chain reaction (PCR) and high-resolution melting analysis (HMR) for various molecular biology applications. It has a unique design with a rotor that spins the samples, which minimizes the optical and thermal variation. The instrument’s stability in combination with its fast ramping rates and short equilibrium times renders Rotor-Gene Q highly suitable for fast, sensitive and accurate quantitative analyses.

User-friendly design and software

With its small, light and robust design there is hardly any need for maintenance. There is a lifetime guarantee for the LEDs and no need for optical calibration or cleaning of sample blocks. Also, the rotary design prevents any condensation or bubbles forming in the reactions. Rotor-Gene Q can be used with either tubes or Rotor-Discs for faster handling of high-throughput workflows. In addition, it features intuitive software, such as the Q-Rex Software, which supports all analysis procedures from basic to advanced algorithms, and its extension software Rotor-Gene ScreenClust HRM Software, which enables HRM analysis for genotyping, mutation screening, pathogen typing and quantitative methylation analysis. Furthermore, the software REST software 2009 takes the different PCR efficiencies of the gene of interest and reference genes into account and provides analysis of e.g. up- and downregulation for gene expression studies.

Widest optical range — even more applications

Rotor-Gene Q has an unrivaled optical range with up to 6 channels spanning from UV to infrared wavelengths and can therefore be used with a number of different fluorophores. The software also allows addition of new wavelength combinations so that it will be compatible with new dyes to be used in future applications. Today, the instrument can be used for applications such as gene expression analysis, genotyping, pathogen detection, mutation analysis, DNA methylation analysis and miRNA research.

Disruption

Technology Knowledge

Bead-Mill Disruption

Rotor-Stator Disruption

Large-scale sample disruption

Fast release of biomolecules

For information about products based on this technology, see TissueLyser LT and TissueLyser II.

Rotor-Stator Disruption

Small-scale sample disruption

Analysis of nucleic acids and proteins from biological samples are often a crucial part of medical and biochemical applications. Therefore, a fast and efficient method is needed for releasing these biomolecules from biological samples. Usually mechanical, physical, chemical and/or enzymatic methods are used to disrupt the biological matrixes and cells. In low-throughput workflows, rotor-stator disruption is a suitable mechanical method. It’s carried out using a rotor-stator homogenizer, essentially a handheld high-speed blender, which mechanically shears the samples. The shearing is a result of both: the rotation of the blade and the turbulence in the sample. This method is often combined with enzymatic lysis and/or physical disruption using liquid nitrogen for more efficient disruption and homogenization.

Fast release of biomolecules

For information about a product based on this technology, see TissueRuptor II.

Reference Products

TissueRuptor

TissueLyser LT

TissueLyser II

Low-throughput sample disruption

Speed and safety

Multiple downstream applications

Low- to medium-throughput sample disruption

Efficient processing

Quality and versatility

Medium- to high-throughput sample disruption

Efficient processing

Sample Preparation

Technology Knowledge

Magnetic Bead Extraction

Spin-Column Extraction

Single Cell Isolation

Fast and easy purification

A wide range of starting materials

For information about a product based on this technology, see EZ1 Advanced XL and QIAsymphony SP.

Spin-Column Extraction

Fast and efficient purification

A wide range of starting materials

For information about products based on this technology, see QIAcube.

Singe-Cell Isolation

Individual and viable cells

Magnetic technology

For information about products based on this technology, see QIAscout.

Reference Products

QIAcube

QIAcube HT

QIAsymphony SP

EZ1 Advanced XL

QIAscout

Efficient single-cell isolation

Simple and straight-forward

Multiple applications

Mid- to high-throughput nucleic acid purification

Safe and standardized

Simple integration in workflows

Automated and safe sample purification

QIAsymphony SP^TM is a fully automated system that purifies DNA, RNA, bacterial and viral nucleic acids. It can be set up in just a few minutes and processes up to 96 samples in continuous batches of 1-24 samples. The system uses magnetic bead technology to purify the nucleic acids from a wide range of starting materials. It can purify intact long DNA (>25 kb). The system consistently delivers high yields at high recovery rates with exceptional purity, so that the samples are ready to be used for different downstream applications. Contamination is prevented by tip and magnetic head guards as well as UV light while full traceability is ensured by the bar codes used for the samples and reagents.

Outstanding flexibility

The QIAsymphony SP^TM is easy to integrate in existing workflows due to its flexibility. Instrument can handle various type of samples, such as tissues, blood, cell-free body fluids as well as food testing samples. Furthermore, the instrument can accommodate both small and big sample batches, and depending on the application it can be set up for elution volumes ranging between 50 and 500 µl. The setup of the runs also allows considerable flexibility, where up to 4 different protocols can be used in each run Samples can be loaded in-process allowing for urgent samples to be prioritized when necessary. Two different purification kits can be placed it the system at the same time and different protocols, dedicated to these kits, can be used. This means that every batch of samples is run by a defined protocol linked to the dedicated installed kits.

QIAsymphony has 4 channels and maximum of 4 extraction protocols can be defined per run. They will be executed one after another (e.g 10 RNA samples first run, 20 samples Blood genomic DNA etc, they will be processed one after another. Alternatively it is possible to programe all 4 channels to use one protocol in the case of high throughput needs (e.g. 96 samples for extraction of genomic DNA from blood).

Seamless workflow

The automated steps performed by the QIAsymphony SP^TM include the whole purification process, i.e. sample transfer, lysis, shaking, binding, washing and elution. For ease of use and safety and further speed up of the process, it utilizes prefilled reagent cartridges, provides automatic labeling and holds a touchscreen featuring intuitive software. Once the samples have been purified by the QIAsymphony SP^TM module, they are ready to be used for a number of downstream applications. If they are to be used specifically for PCR, the most convenient approach is to automatically transfer the samples from QIAsymphony SP^TM to the QIAsymphony AS^TM module for a PCR assay setup.

Automated nucleic acid purification

Safety and accuracy

Traceability and versatililty

Sample preparation for low-throughput needs

QIAcube performs fully automated purification of DNA, RNA or proteins using QIAGEN spin-column kits, and can purify up to 12 samples per run. It follows a simple lyse, bind, wash and elute procedure and eliminates all manual steps usually necessary for purification. It swiftly purifies double- or single stranded DNA fragments from 100 bp to 10 kb as well as 6xHis tagged proteins. The sample preparation is standardized giving rise to high yields of high quality samples in a reproducible manner. Tests have proven that there is no sample carryover. These qualities thereby render the instrument suitable for research laboratories in the fields of pharmacology, biotechnology and biomedicine. It is recommended for downstream applications such as sequencing, gene expression analysis, genotyping and proteomics.

Versatile high quality purification

The QIAcube can be used for a wide range of starting materials, e.g. to purify plasmid DNA from E. coli cultures, DNA from amplification reactions and also from agarose gels, genomic DNA from blood or body fluids, viral nucleic acids from plasma, serum or cell-free body fluids, total RNA from animal cells and RNA samples, 6xHis-tagged proteins from E. coli cultures or eukaryotic cells as well as enable depletion of serum proteins from serum or plasma. In total, more than 60 different QIAGEN spin-column kits can be automatically processed by the QIAcube with 150 predefined protocols.

Simple integration in workflows

The process can easily be integrated into more complex workflows as there are integrated safety features, such as load checks designed to ensure that all labware and accessories are fitted correctly. The software has a user-friendly interface and can be operated without any previous knowledge. Since QIAcube does not require an external PC and is preinstalled with protocols for the purification mentioned above, the purification setup is exceptionally simple and saves valuable space in the laboratory.

Quality Control

Technology Knowledge

Spectrophotometry

Capillary Electrophoresis

High resolution separation of biomolecules

Downstream applications

For information about a product based on this technology, see QIAxcel Advanced.

Spectrophotometry

Measuring quantity and quality

Reproducibility and linearity

For information about products based on this technology, see QIAxpert.

Reference Products

QIAxpert

QIAxcel Advanced

Fast check of nucleic acids

High reproducibility

Intuitive software

Rapid and reliable DNA and RNA analysis

Software for easy quality control and quantification

Wide range of applications

Assay Setup

Technology Knowledge

Liquid Handling

Automated Sealing

Bead sealing for reproducible qPCR

Safety and flexibility

For information about products based on this technology, see TubeSealer.

Liquid Handling

Automation for accuracy

Reproducible pipetting

For information about products based on this technology, see QIAgility, QIAsymphony AS

Reference Products

QIAgility

QIAsymphony AS

TubeSealer Module

TubeSealer module enables automated qPCR tube sealing

Pure reliability

Exceptional flexibility

TubeSealer MORE DETAILS

High-precision automated PCR setup

Pure pipetting accuracy

Flexibility and applications

Automated PCR assay setup -Seamless integration with QIAsymphony SP

The QIAsymphony AS is a module that directly interfaces with QIAsymphony SP. Any samples that have been purified with QIAsymphony SP can be automatically transferred to the QIAsymphony AS module for PCR assay setup, a so called integrated run. In order to make sure that the process is fully traceable, a bar code system is utilized, labeling the samples all the way from crude starting material to the final PCR sample. This is enabled by the complete bi-directional data exchange capability between the modules, which also ensures that all the data are fully traceable and available to the user.

Since manual pipetting steps are eliminated, the quality and efficiency of the assays can be ensured even for complex PCR assays that need to be set up on a routine basis. With dedicated software and validated protocols, it is easy to use and allows high-throughput, reproducible workflows at the highest possible quality standards.

Accurate and flexible workflow

The accuracy of the system is additionally ensured by featuring a full temperature control, which actively cools the templates, reagents and reactions mixes. An inventory scan is performed before each run, checking the consumables and liquid levels, reading the bar codes of the reagent cartridges and preventing loading errors. All these functions are combined with features that enhances QIAsymphony flexibility. For example, several different PCRs, like multiplex PCR, pathogen identification, food safety assays or STR tests can be set up during each run and the system can even normalize/dilute the eluates to given target concentrations.

Detection

Technology Knowledge

Capillary Electrophoresis

Real-Time PCR

Pyrosequencing

Next-generation Sequencing

Monitoring DNA amplification

Sensitivity and accuracy

Downstream applications

For information about products based on this technology, see Rotor-Gene Q.

Next-generation Sequencing

From single DNA sequences to massively parallel sequencing

Sequencing technologies

Under the NGS label, we can include the so called second, third and fourth generation sequencers. Nowadays, there are several technologies utilizing a variety of methods, as for example:

Illumina — sequencing by synthesis (bridge amplification) and detection of fluorescence signals
Ion Torrent — sequencing by synthesis (emulsion amplification) and detection of changes of pH by an ion semiconductor
Pacific Biosciences — single-molecule real-time sequencer
454 Life Sciences — sequencing by synthesis (emulsion amplification) and detection of pyrosequencing signals
SOLiD — sequencing by ligation (emulsion amplification) and detection of fluorescence signals
Qiagen GeneReader — sequencing by synthesis (emulsion amplification) and detection of fluorescence signals
Oxford Nanopore — Nanopore DNA sequencing

Sequencing workflow

NGS workflow is a complex process which involves several steps. A typical workflow includes:

Nucleic acid extraction
Fragmentation and quality control (QC)
Target enrichment (optional) and QC
Library preparation and QC
Clonal amplification (optional)
Sequencing
Data analysis and interpretation

NGS is used for different applications, such as whole genome and whole exome sequencing, transcriptome profiling, targeted DNA re-sequencing, epigenomics, etc.

NGS workflow key points

Nucleic acid extraction

Target enrichment

Sequencing

Library preparation

Clonal amplification

Data analysis and interpretation

For information about an NGS workflow based on this technology, see Qiagen GeneReader NGS.

Pyrosequencing

Shedding light on DNA sequences

Efficient chemistry

For information about products based on this technology, see PyroMark.

Capillary Electrophoresis

High resolution separation of biomolecules

Downstream applications

For information about a product based on this technology, see QIAxcel Advanced.

Reference Products

QIAxcel Advanced

Rotor-Gene Q

PyroMark Platforms

GeneReader NGS

The first complete NGS workflow in one system

The GeneReader NGS System has been designed to perform the whole next-generation sequencing (NGS) workflow: from nucleic acid extraction to DNA library preparation, from sequencing to data analysis. The system consists of several modules: the QIAcube Classic for DNA purification and library preparation, the GeneRead QIAcube for clonal amplification step of library template preparation, the GeneReader instrument for DNA sequencing and the PowerStation for data analysis and traceability. The GeneReader platform performs fluorescence-based sequencing according to unique reversible terminated and fluorescent-labeled dNTPs in a sequencing-by-synthesis paradigm.

Efficient sequencing chemistry

The sequencing part in the GeneReader NGS System consists of several steps: the library DNA fragments are first clonally amplified on sequencing beads generating single strand DNA templates. These are then allowed to hybridize with a sequencing primer giving rise to primer-template carrying beads. Subsequently the beads are deposited onto a surface-coated flow cell and covalently linked to a glass slide generating a high-density array. The flow cell is then loaded into the GeneReader sequencer where the array of DNA fragments is subjected to reagents containing unique reversible terminated and fluorescent-labeled dNTPs. The sequencing chemistry uses four dye colors for labeling, one for each different DNA base, and the reversible terminators allow the addition of a single engineered nucleotide to each single DNA template. After each addition of dNTPs, the array is scanned and the fluorescence of the four dyes is recorded. At the end of each cycle the dyes and the reversible terminators are cleaved off, allowing the next cycle of dNTPs incorporation to follow. Once the sequencing has been finalized, the GeneReader software provides the sequence information in a FASTQ file format to be analyzed by the QCI Analyze software, in order to generate a variant analysis report.

Versatile process with multiple applications

The process can easily be adapted to the user’s needs. The batch sizes are scalable and the system also allows continuous loading as well as the use of multiple flow cells. When it comes to applications, the GeneReader NGS System can be used to provide fast and deep knowledge in cancer research using gene panels such as the GeneRead QIAact Actionable Insights Tumor Panel, which can detect 1,250 clinically relevant genetic mutations, as well as the GeneRead QIAact BRCA 1/2 DNA panel and the GeneRead QIAact Lung DNA and RNA panels, for somatic and fusion variant analysis. Moreover the release of the GeneReader QIAact DNA Custom Panels pipeline leverages the GeneReader NGS System flexibility in meeting any customer need.

Rapid and reliable DNA and RNA analysis

Software for easy quality control and quantification

Wide range of applications

Precise and robust real-time PCR

User-friendly design and software

Widest optical range — even more applications

Quantifying sequence variations with pyrosequencing

From pyrosequencing to analysis reports

Case Studies

Spin-Column Nucleic Acid Purification

Next-Generation Sequencing

Consumable Cartridge

Magnetic-Bead Nucleic Acid Purification

How can we help?

Touch base with us

Whether you are looking for new technical approaches to automate laboratory workflows, you need to ensure regulatory compliance of your product, or you want to reduce costs and shorten the time-to-market, we have the tools to ensure your business growth. We specialize in turning ideas into cutting-edge solutions, so simply contact us and tap into our technology and application knowledge.

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Management Team

Patrick Widler (CCO)
Michael Collasius (CEO)
Konstantin Lutze (CTO)

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Who trusts in us

Customer Testimonials

"Our clients have diverse needs, and the partnership with HSE•AG enables us to successfully match system development needs with innovative solutions. We can tap into HSE•AG’s wealth of experience in systems development, automated workflow solutions, applications, and industrialization to develop customized solutions and help our customers bring products to market."

Colin A. Baron, MBA

Chrysalis Biomedical Advisors, Inc.

"HSE•AG is a premier service provider for system design and development in the life sciences and diagnostics. The highly engaged HSE•AG team delivers unique solutions and the best service to customers, making them a reliable and competent partner. HSE•AG’s agility and expertise, resulting from extensive experience in developing full workflow solutions, have contributed very significantly to our business growth. QIAGEN’s mission of “making improvements in life possible” has significantly benefitted from HSE•AG’s capabilities and we look forward to further successes."

Peer Schatz, CEO

QIAGEN N.V.

“In HSE, we have found an expert partner for the development of a complex microfluidic interface and its integration into our modular cell analysis platform."

Marco Di Berardino, Founder

Amphasys

"HSE•AG is a highly experienced team that has developed a wide range of revolutionary solutions for the life science tools and diagnostics industries."

Thomas Schweins, Senior Vice President, Life Science Business Area and Human Resources

QIAGEN N.V.

What makes us special

Our Expertise

Applications & Technologies

Key application and systems engineering knowledge in next-generation sequencing, PCR, and capillary electrophoresis

Workflows & Processes

We have successfully combined a variety of technologies into complete laboratory workflows including full data integration

Project Management & Engineering

Our passion is to provide you with broad engineering and agile project management competencies

What we have to say

Blog categories

Comments

Our References

Technology Know-How & References

Select workflow step

All

Technology Knowledge

Bead-Mill Disruption

Large-scale sample disruption

Fast release of biomolecules

Rotor-Stator Disruption

Small-scale sample disruption

Fast release of biomolecules

Magnetic Bead Extraction

Fast and easy purification

A wide range of starting materials

Spin-Column Extraction

Fast and efficient purification

A wide range of starting materials

Singe-Cell Isolation

Individual and viable cells

Magnetic technology

Spectrophotometry

Measuring quantity and quality

Reproducibility and linearity

Capillary Electrophoresis

High resolution separation of biomolecules

Downstream applications

Liquid Handling

Automation for accuracy

Reproducible pipetting

Automated Sealing

Bead sealing for reproducible qPCR

Safety and flexibility

Real-Time PCR

Monitoring DNA amplification

Sensitivity and accuracy

Downstream applications

Pyrosequencing

Shedding light on DNA sequences

Efficient chemistry

Next-generation Sequencing

From single DNA sequences to massively parallel sequencing

Sequencing technologies

Sequencing workflow

NGS workflow key points

Nucleic acid extraction

Target enrichment

Sequencing

Library preparation

Clonal amplification

Data analysis and interpretation

Reference Products

Low-throughput sample disruption

Speed and safety

Multiple downstream applications

Low- to medium-throughput sample disruption

Efficient processing

Quality and versatility

Medium- to high-throughput sample disruption

Efficient processing

Case Study QIAcube

The Challenge

The Goal

The Approach

The Result

Mid- to high-throughput nucleic acid purification

Safe and standardized

Simple integration in workflows

Case Study QIAsymphony

The Challenge

The Goal

The Approach

The Result

Case Study QIAsymphony Cartridge

The Challenge

The Goal

The Approach

The Result

Automated nucleic acid purification