PCR Frequently Asked Questions 
Select the product group below to get answers to common product questions. If you need additional help, our Scientific Support group is ready to assist you. Your feedback will help us provide products and services that respond to your needs. Please select the category your comments are most closely related to, so we can direct your comments appropriately. Can the IsoSafe be cleaned in a dishwasher? Can the IsoSafe be cleaned in a dishwasher? Can you tell me the depth and the diameter of the bores of the exchangeable thermoblocks? Does the thermoblock for microtest plates have a lid? Can 24-well cultivation plates be used in the exchangeable thermoblock for MTPs and deepwell plates? Which slides fit into the exchangeable thermoblock for 4 slides (Order no. 5368 000.010)? Is the exchangeable thermoblock for slides compatible with the Eppendorf DualChip Microarrays? Can the IsoRack be centrifuged? Are the cool packs (Isopack) of the IsoTherm-System available individually? Can the IsoSafe be cleaned in a dishwasher? Can the IsoSafe insulation box of the IsoTherm-System be autoclaved? Are the IsoPacks resistant to sodium hypochloride (NaOCl)? How long do IsoPacks (white, blue) maintain their temperature? Do the IsoRacks fit upon the SmartBlocks for microreaction tubes (0.5 mL; 1.5 mL; 2.0 mL)? Can the in situ Adapter be used with the Mastercycler®? Do you have an application for the Eppendorf in situ Adapter? Can the Are batch-specific certificates for the new purity grades available in the internet? Are Eppendorf products free of RNA? Why are there new Eppendorf purity grades in 2012? Have the products changed with the new purity grades? Which purity grades will be modified from 2012? Is it possible that nitrogen from the tube material penetrates my sample? Do the Eppendorf PCR consumables have a special grade of purity? Can the deep well mats be autoclaved? Does the blister packaging of the Biopur products contain latex? How do you make your Biopur products free of pyrogens? Which of the Eppendorf PCR 96 Plates can be sealed with the heat sealer? What is the best sealing procedure for storing plates at - 80 °C? What is the best way to seal a PCR plate? Can I perform relative quantification with the Mastercycler ep realplex? What are the key benefits of the Mastercycler ep realplex? Can I run my established protocols on the Mastercycler ep realplex? How fast is the Mastercycler ep realplex silver or aluminium block? Is there an even excitation of the LEDs over the 96 positions? Can ROX be used for normalisation? Does the Mastercycler ep realplex require any specific chemistry? What kind of tubes can I use with the Mastercycler ep realplex? What is the excitation source of the Mastercycler ep realplex? Is the Mastercycler ep realplex capable of multiplexing? How long does it take to detect all 96 samples? Can I perform gene expression analysis with the Mastercycler ep realplex? What is the bandwidth for every filter? It is possible to detect more than one dye per filter during a single run? Is the Mastercycler ep realplex 21 CFR Part 11 conforming? Is it possible to extend the number of USB interfaces? What is the Self Test Function? Is it possible to check the mastercycler pro with an external measurement system?
No.
No.
The specification can be found within Userguide 001: "Applications for Thermomixer comfort, Thermomixer compact and ThermoStat plus".
Yes. When the exchangeable thermoblock for MTP block is ordered, the lid is delivered in the same packaging. It can also be ordered separately (order no.: 5363 000.217).
No. The thermoblock for MTP is designed for the globally recognized standard microplate with dimensions of 127 x 86 mm. The microtiter plates for cultures have larger dimensions (132 x 88 mm) and therefore do not fit in this block.
The exchangeable thermoblock 'slides' can be used for all glass slides of 75-76.5 mm length, 25-26 mm width and a height of up to 1.2 mm. This thermoblock is well suited for all types of hybridization reactions such as microarray hybridization or fluorescence in situ hybridization (FISH). Application notes descibing the use of thermoblock 'slides' for those kind of applications can be found on our homepage
No. For the DualChip Microarrays, an exchangeable thermoblock is required that applies additional pressure to the hybridization frames. This reduces potential evaporation to a minimum.
Please note that we offer a special IsoRack adapter for our 5810/R (swing-bucket rotor type A-4-81, flex buckets). In addition, the IsoRacks can also be centrifuged in the A-2-DWP and in the A-4-62-MTP. In this case, centrifugation is limited to a max. rotational speed of 3,700 rpm (max. 1,000 centrifugations).
No.
No.
Nein.
They are made of polyethylene and filled with a special, non-toxic liquid. The bottom is covered with an aluminum foil.
NaOCl attacks the aluminum foil (for both packs sizes) slightly. Over a period of eight hours or more, this may lead to damage. The IsoPack polyethylene housing is chemically resistant to NaOCl. Even if a leak occurs, the liquid in the IsoPack is non-toxic.
They are made of polycarbonate.
If IsoPacks (in an IsoRack) are sealed in an insulating box (IsoSafe), a temperature of 0 °C (in the white packs) can be maintained for at least 6 hours and –21 °C (in the blue packs) for > 3 hours.
If the IsoPacks are in an open insulating box, 0 °C can be maintained for roughly 4 hours and –21 °C for 1–2 hours.
If the IsoPacks/IsoRacks are not placed in an insulating box, a temperature of 0 °C can be held for 1.5–3 hours and –21 °C can be held for 0.5–1 hour.
No. The IsoRacks fit only upon the Thermoblocks for the older devices Thermomixer comfort, Thermomixer compact & ThermoStat plus.
The in situ Adapter can be used with the Mastercycler® and the Mastercycler® gradient. Due to its size, the adapter cannot be used with the Mastercycler® personal.
In the journal Biotech International, A Reed Elevia Publication, June 2000, Volume 12, No. 3 there is an application published under the title "Single Copy Virus detection by Gene point in situ Hybridisation on the Eppendorf Mastercycler®".
The
Yes, the batch-specific purity grades can be downloaded at www.eppendorf.com/certificates.
Due to the modularization of purity grades, some products are labeled with more than one purity grade symbol. For example, the epDualfilter T.I.P.S. has the double seal "PCR clean "+ "Sterile" and the UVette the double seal "PCR clean" + "Protein-free" on the packing. The certification remains unaffected by the modularization.
All products certified with "PCR clean" are tested free of human DNA, DNase, RNase and PCR inhibitors. The following applies from our point of view: Where no human DNA is detected, there can also be no RNA, which is considerably more unstable.
The previous purity grades were developed due to customer requirements and new applications, in the course of the years. To meet the customer requirements for single applications even better, Eppendorf has extended the certification of the purity grades "Sterile" (now, also certified as free of pyrogenes) and "Biopur" (now, also certified as free of DNase and PCR inhibitors). In addition, the previous purity grades have been transferred to a new modular system that provides the same variety and flexibility and yet is readily understandable.
No, they are the same products as before, i.e. all specifications as dimensions remain the same. Only the packing has changed, due to the new seals. In addition, the certification of "Sterile" and "Biopur" has been extended but the entire production process was maintained.
For all purity grades, there will be new packing seals. In addition, there will be a further certification for the purity grades "Sterile" and "Biopur". "Sterile" will certify sterility and also the freedom of pyrogenes. The purity grade "Biopur" also includes the freedom of DNase as well as of PCR inhibitors.
Yes, if no batch attachment is required for the application, products of the old and new modular purity grades can be used, as their specifications are the same.
No. The propylenes which we use are materials of foodstuff quality. It is tested according to the directives for materials which come into contact with foodstuffs of the German Federal Office of Health and has no nitrogen-containing components.
Yes. We certify our PC plates and sealing options with "PCR-Clean". This certificate stands for guaranteed freedom from human DNA, DNase, RNase and PCR inhibitors.
Yes. They can be autoclaved (1 bar, 20 minutes, 121 °C).
Yes. With the "Pierce-it-Lite" heat sealing foil from Eppendorf this is possible without problems!
No, the blister packaging is free from latex.
All Biopur products are manufactured fully automatically under cleanroom conditions. This eliminates contamination of the disposables through contact with people. Additionally the products are sterilized by radiation or treatment with ethylene oxide. An independent laboratory checks that each individual batch is free of pyrogens.
All plates listed in the Eppendorf catalog can be sealed with the heat sealer.
Heat sealing is the only method which enables a 100% hermetic sealing. We recommend using the heat sealer and the Peel-it-Lite heat sealing foil from Eppendorf, which is suitable for storage temperatures down to – 200 °C. To recover the products, the sealing is simply removed manually.
The heat sealer from Eppendorf in combination with heat sealing foils or films offers the best sealing. Another effective method is to use Eppendorf cap strips. For sealing with cap strips, we recommend using the capping aid, an inexpensive tool for producing a very effective seal as cannot be obtained by setting on the caps with the fingers alone.
Yes, a data analysis module for relative quantification (DDCt method) is included in the software.
The Mastercycler ep realplex brings advanced real-time PCR technology to the benchtop with its highly intuitive operation and analysis software, and its extremely robust, compact design. The realplex combines the advanced, high speed gradient thermal block design of the Mastercycler ep thermal cycler family with highly sensitive optical detection technology of wide dynamic range so you can analyze more samples with greater flexibility in a single plate.
Established protocols can easily be adapted to the Mastercycler ep realplex. The temperature ramp rates can be fine-tuned to mimic the characteristics of other qPCR platforms. Furthermore, the realplex’s gradient capabilities enabling you to test a range of temperatures across 12 columns of the plate.
Heating speed: silver 6°C/s aluminium 4 °C/s Cooling speed: silver 4.5°C/s aluminium 3 °C/s
Through an intensive factory calibration process, all positions of the 96-LED array are normalized for even excitation across the sample plate.
Due to our optical concept (96-LED array) a ROX normalisation is not necessary.
The Mastercycler ep realplex is an open system that does not require or prefer any specific chemistry. All intercalating dyes or probe-based detection formats are supported.
All standard plates or tubes with optical flat sealing can be used.
The Mastercycler ep realplex uses a 96 LED array with an excitation wavelength of 470 nm, which is able to effectively excite the most common dyes used in real-time PCR.
Yes, the Mastercycler ep realplex is capable of multiplexing. With the realplex2, duplex assays can be performed while the realplex4 can be used for up to 4 x multiplexing.
With one dye per filter wheel, 8 seconds are required for data acquisition. The measuring time is extended to 16 seconds with two dyes per filter wheel, as required by the realplex4.
Yes, a data analysis module for relative quantification (delta delta Ct method) is included in the software.
520nm ± 10nm 550nm ± 10nm 580nm ± 5nm 605nm ± 15nm
No, it is not possible to define more than one dye per filter for a single run.
The Mastercycler ep realplex enables GLP-compliant documentation of all real-time PCR and device data, but it is not 21 CFR Part 11 conforming.
Yes! With the new Control Panel (with 2 USB interfaces) up to 5 Mastercycler pro and/or Mastercycler ep can be run together in a minisatellite system with any numeral configurations. With the CycleManager pro software up to 30 Mastercycler pro and/or Mastercycler ep can be run together in a network with any numeral configurations. Please contact your local Eppendorf contact.
Yes! It is only necessary to perform a software update of the Control Panel and the Mastercycler ep device(s). Please contact your local Eppendorf contact.
Yes! In principal, PCR single tubes, 8-tube strips or plates can be used on the Mastercycler pro as long as they have the SBS standard format.
Yes! The number of USB interfaces can be extended by means of a USB Hub.
The self test function permits a quick check regarding the following attributes of the Mastercycler pro thermoblock without requiring an external measurement system:
• Heating and cooling rates
• Correct function of the temperature control circuit
• Temperature homogeneity within each of the three block zones (left, middle and right zone)
• Temperature homogeneity throughout the whole block.
After a passed self test a certificate in PDF format can be generated.
The optionally available self test USB key activates the self test function on the Control Panel for all connected Mastercycler pro.
The selftest function is an additional tool to check the thermoblock for alteration, maladjustment or malfunctioning, however, a temperature verification by means of an external measurement system is not replaced by the selftest function.
Eppendorf offers a temperature validation system with which the user can test the Thermocycler himself. However, it is also possible to have this done by Technical Service. For further information please call your local Eppendorf contact.
Programs, protocols and log-files can be exported to a USB flash drive or Multi Media Card (MMC). The user can select between a text-only format (.TXT) and PDF. |
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