Eppendorf (company)

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Eppendorf is a biotechnology company, originally based in Hamburg/ Germany. The company was founded in 1945 in a small building at the university hospital of Hamburg. Nowadays, it's a global player in the biotech community, employing nearly 2000 people. Eppendorf offers a broad range of biotechnology equipment including centrifuges, pipettes, thermocyclers, thermomixers, devices for micromanipulation, consumables, microarrays, and full-automatic workstations for liquid handling.

 One of the most famous products is the microcentrifuge tube - a small conical-bottom tube (approx 1.5 ml), which is used to store a small amount of liquid. Many other companies copied these tubes and offer them, very similar to those of the Eppendorf brand, but they are all commonally known as eppendorfs or called "eppi tubes" in laboratory slang all over the world. They are frequently used in research areas such as tissue culturing and molecular biology. Many centrifuges have been specifically designed to hold eppendorf tubes.

Eppendorf is also known for its pipetters. Often the phrase "Eppendorf" is used in reference to micropipetting, regardless of the brand used in the lab.

Eppendorf Biochip Systems

Eppendorf & microarrays

Recently, Eppendorf founded a company called Eppendorf Biochip Systems [1], which specializes in microarray solutions for routine applications, including DNA microarrays for gene expression analysis, detection of infectious agents, GMOs in food and feed, and miRNA analysis. Furthermore, transcription factor microarrays and protein microarrays are offered as well as a novel colorimetric detection system, the so-called Silverquant scanner and Silverquant labeling kit. Customized solutions for drug discovery and other screening-type or higher throughput applications are the core of the offering.

Description of Products

DualChip gene expression

The DualChip for gene-expression is a series of pre-defined, topic-specific low-density microarrays. The topics are related to human medical research like inflammation, apoptosis, cancer, aging, signaling, DNA damage, or metabolic syndrome. The 70 to 300 genes are chosen in cooperation with research-people who are working in that area. The genes are located in triplicates on the chip to prove the results. The usage of small pre-attached hybridization frames garanties reliable results and easy usage. The semi-customized concept enables the user to choose one pre-defined microarray and add up to 20 genes of interest. A customized microarray contains up to 300 genes of interest, inclusive the DualChip control system. For the labeling process, the researcher can use direct fluorescence, indirect fluorescence, biotin, as well as Silverquant.

Silverquant - colorimetric detection

The most commonly used labeling/ detection technology for microarrays is the fluorescence. This technique is known to nearly all microarray users. The usage of fluorescence-dyes has at least one disadvantage: The molecules are light-sensitive. There are some stabilization reagents available, and the user should work in a lab without windows but this kind of prevention is suboptimal. To avoid any kind of bleaching, the silver-staining-procedure which is known for protein-gels for a long time is an optimal procedure. The colorimetric Silverquant technology has adapted the classical silver-staining process with the microarray-technology. This colorimetric staining allows the detection of any biotinylated biomolecules providing light grey-to-black spots that can be visualized first by the naked eye and then subsequently scanned and quantified with the Silverquant scanner and scanning software. The grey level intensity is related to the quantity of target molecules that are hybridized onto the spot. The Silverquant analysis software processes the quantified data (normalization of data).

Normalization process for gene expression on low-density arrays

For an adequate data normalization, a two-step-process was developed, using a group of spike-in controls (Internal Standard RNA) as well as a group of up to 13 housekeeping-genes. The normalization of fluorescence data is done by an evaluation software which is adapted to the DualChip concept. Silverquant-based data are normalized by the Silverquant analysis software.

Transcription factor analysis

One step after the gene-expression analysis is the analysis of specific transcription factors. Those factors are protein molecules which contains a DNA-binding region. This recognition region is specific to a more or less specific sequence on the DNA-strand. By binding to its target region on the DNA-strand, the transcription factor (TF) may activate or repress the transcription which is done by the RNA-polymerase-II (eucaryotes). One of the best studied cell signaling pathways is the MAPK (Mitogen-Activated Protein Kinases) pathway, which regulates major cellular functions such as cell growth, differentiation, immune-mediated inflammatory responses, and apoptosis. The TF Chip MAPK was developed to analyze the 8 eight main TFs from the MAPK pathway (Elk-1, c-Jun (AP1), ATF-2 (CREBP1, CREB2), MEF2, STAT1, c-Myc, p53, and NFATc1 (NFATc)) in parallel – it provides more information than ELISA or other alternative methods can. The unique technology of the TF Chip MAPK reveals more about the biological activity of the TFs by selectively detecting the activated form of these transcription regulatory proteins, which are simultaneously bound to their specific recognition site of double-stranded DNA.

GMO microarrays

The DualChip GMO microarrays allow the detection of EU-approved GMOs by identifying their genetic elements. This system also enables the screening of other GMOs that contain corresponding transgene elements (approx. 60% of all GMOs worldwide). The simultaneous detection of GMO-specific elements, comprehensive controls, and plant-specific markers take GMO screening tests to another level. The technology is based on a PCR reaction followed by hybridization on a predefined GMO microarray. The DualChip GMO kit includes all of the components required after DNA extraction allowing the straightforward processing of 16 individual tests with a sophisticated internal control system. The DualChip GMO is suited for detection and scanning by the Eppendorf Silverquant® system. The transgene elements are visualized and analyzed quickly and easily, and the evaluation software tool that is provided with the kit generates accurate results and corresponding report files with just a few clicks.

In collaboration with the Joint Research Centre (JRC) of the European Union, Eppendorf conducted a validation study with Eppendorf’s DualChip® GMO microarray. A detailed description of the technology and the study can be found at http://bgmo.jrc.ec.europa.eu/home/docs.htm. The validation study was carried out within a European framework project (Co-Extra project) with the participation of 12 laboratories from 8 European countries working on GMOs. The results of the study clearly demonstrate the high reproducibility, accuracy and sensitivity of the technology. The DualChip GMO kit is the first fully validated microarray-based technology for the screening of GMOs. The selection of the detectable organisms can be extended according to the growing number of approved and unapproved GMOs which have to be screened in the near future.