Powered by proprietary CAT5™ technology, the DNAstorm™ FFPE extraction kit enhances the removal of formaldehyde-induced damage and provides DNA with higher yield and quality and greater amplifiability. The DNAstorm™ kit is the best solution for next-generation sequencing and other advanced applications.
The DNAstorm™ FFPE Kit is now also available in MagBead format - no centrifuge required for DNA isolation.Buy Product Information Sheet
The DNAstorm™ kit offers a convenient workflow (spin-column or MagBead-based) for efficient extraction of high-yield and high quality DNA from FFPE samples.
The kit can also be combined with the RNAstorm™ FFPE kit to obtain pure DNA and RNA from the same tissue section.
DNA from four different FFPE tumor samples (colorectal, lung, bladder, and esophagus) was extracted using the DNAstorm™ FFPE kit along with a popular competitor's kit. Equal amounts (500 ng) of DNA were loaded and run on a pulsed field gel. Significant improvements in average DNA size are seen using the DNAstorm™ kit.
|Applications||Next generation sequencing, PCR, qPCR/RT-PCR|
|Kit format||Manual (50 spin columns) or MagBeads (96 extractions)|
|RNase treatment step||Included|
|Input samples||Formalin-fixed samples (paraffin embedded or in fixative)|
|Recommended input sample amount||1-4 sections (5-10 µm each)|
|Isolation time||50 minutes hands-on time|
|Each kit includes:||Spin Columns or MagBeads
CAT5™ Lysis Buffer
Contamination from RNA is eliminated by performing an optimized RNase digestion step immediately following the lysis step.
The biggest variable that affects the total amount of DNA obtained is the quality of the sample itself (i.e. the type and amount of tissue, and the care taken in isolation and preservation of the sample). Using the DNAstorm™ kit, and assuming at least reasonable sample quality, amounts greater than 1 µg can be obtained.
Yes. Good quality libraries can be obtained, providing that the DNA is of sufficiently high quality.
Use a microtome to obtain 5-10 µm sections from FFPE samples. Sections thinner than 5 µm may be used if they can be reliably cut. Sections thicker than 10 µm are not recommended because they may not be fully digested.
Yes, tissue can be used which is not embedded in paraffin. In this case, we recommend mechanically grinding an amount of tissue equivalent to the recommended number of sections.
Yes, FFPE cores can be used. Because cores are not processed using a microtome, sample digestion tends to be more difficult and mechanical homogenization (e.g. using steel beads) is recommended if incomplete digestion is observed.
The DNAstorm™ kit includes a recommended Deparaffinization Reagent. Unlike other common methods (e.g. xylenes), the Deparaffinization Reagent is efficient, non-toxic and does not require the use of a fume hood. In our testing, the included reagent is at least as effective as xylenes at removing paraffin and allowing purification of high quality nucleic acids.
The white cloudy layer is an emulsion between the Deparaffinization Reagent and the CAT5 Lysis Buffer, which may form when these two reagents are vortexed or given a hard mix. To avoid this issue, we recommend not vortexing the sample when the Deparaffinization Reagent and CAT5 Lysis Buffer are in contact. When mixing is necessary in the presence of both these reagents (e.g. when protease is added), we recommend pipette mixing. The white cloudy layer can be removed by giving the sample a hard spin at maximum speed (> 16,000 x g) for at least 2 minutes. The length of time will depend on the volume of the emulsion.
Due to the wide size distribution of DNA isolated from FFPE tissue samples, we recommend using pulsed-field gel electrophoresis (PFGE). Methods based on capillary electrophoresis such as the Agilent BioAnalyzer can also be used, but may not properly resolve high molecular weight fragments (greater than 10k) in better-quality samples.
PCR inhibition is often observed when high amounts of FFPE-extracted template DNA are used. The inhibition is usually not due to the presence of contaminants, but results from residual chemical modifications and damage in the DNA itself. Several simple adjustments to the PCR protocol can overcome this issue. First, the amount of template DNA should be decreased. Second, the amount of PCR polymerase should be increased by 2-4x. Third, the annealing and extension times should be extended. Fourth, the amount of dNTPs can be increased.
An in-depth discussion of this issue is found in Dietrich et al. (2013), PLoS ONE 8(10): e77771.