For automated purification of RNA from FFPE tissues using the EZ2 Connect


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EZ2 RNA FFPE Kit (48)

Cat. No. / ID:  959734

For 48 preps: EZ2 RNA FFPE cartridge, disposable filter-tips and tip-holders, tubes, Paraffin Removal Solution, DNase Booster, RNase-free DNase I, RNase-free water
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The EZ2 RNA FFPE Kit (48) is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.
The EZ2 RNA FFPE Kit is intended for molecular biology applications. This product is not intended for the diagnosis, prevention, or treatment of a disease.

✓ 24/7 automatic processing of online orders

✓ Knowledgeable and professional Product & Technical Support

✓ Fast and reliable (re)-ordering


  • Recovers large amounts of amplifiable RNA
  • Removes paraffin without using xylene or similar solvents
  • Pretreatment-to-elution workflow is fully automated on the EZ2 Connect
  • End product is highly suitable for downstream real-time RT-PCR, NGS or digital PCR (dPCR)

Product Details

The EZ2 RNA FFPE Kit purifies large amounts of amplifiable RNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. This kit's protocol is fully automated from pretreatment to elution using the EZ2 Connect.


There are two ways that the EZ2 RNA FFPE Kit makes RNA extraction more efficient: First, it removes paraffin without multiple wash steps. This reduces the risk of losing sample material and the RNA they hold. Second, it fully automates all procedures after the deparaffinization step, so the number of tedious hands-on steps are radically reduced.


To remove paraffin from the FFPE tissue sample, add Paraffin Removal Solution to the sample sections, vortex for 10 seconds, centrifuge briefly, then incubate for 3 minutes. Your manual procedure ends here.

Transfer the tubes containing the sample sections into the EZ2 Connect, set up and start the run (see “ Fully automated, from pretreatment to elution”).

If you enabled QIAsphere connectivity in your EZ2 Connect, you will receive a notification on your desktop or mobile device when the run is finished.

See figures


The EZ2 RNA FFPE workflow is largely automated. All steps except deparaffinization actually happen during the EZ2 Connect run. When the run is over, the eluate that you take out of the instrument is suitable for downstream real-time RT-PCR, dPCR or NGS.

Supporting data and figures


ApplicationsRT-PCR, dPCR, NGS
Main sample typeFFPE tissue samples
Elution volume50 or 100 µl
Purification of total RNA, miRNA, poly A+ mRNA, DNA or proteinRNA
ProcessingAutomated with an EZ2 Connect instrument
Number of preps per run1–24 samples per run
TechnologyMagnetic particle technology
Sample amountTissue sections, each with a thickness of 5–10 µm, for a total volume of 4 mm3


Quick-Start Protocols (1)
Kit Handbooks (1)
EZ2 RNA FFPE Handbook
PDF (589KB)
Safety Data Sheets (1)
Certificates of Analysis (1)


How do I proceed if the amount of starting material cannot be calculated in detail?
If this is the case, please start out with no more than 2 tissue sections.
FAQ ID - 3943
What size of RNA can be expected?
This can vary significantly and strongly depends on the RNA quality present in the original FFPE sample. Formalin-fixation, paraffin-embedding and storage conditions are factors that affect the RNA size distribution and may cause significant fragmentation of nucleic acids. To limit the extent of nucleic acid fragmentation, be sure to:
Fix tissue samples in 4%–10% formalin as quickly as possible after surgical removal, use a fixation time of 14–24 h (longer fixation leads to more fragmentation, reducing performance in downstream assays).
Thoroughly dehydrate samples prior to embedding (residual formalin can inhibit proteinase K digestion).
Store FFPE tissue samples at -20°C, if possible.
FAQ ID - 3942
When should I use the standard vs. the fast protocol for the EZ2 RNA FFPE Kit?
The FFPE RNA fast protocol provides a streamlined and time efficient workflow for the extraction of RNA to be used in downstream applications like NGS. If longer decrosslinking is required, the standard protocol offers an extended crosslink removal step. Note that incubation at elevated temperature may impact RNA integrity. This longer protocol results in a higher yield, which is beneficial for PCR reactions but might be less suited for NGS.
FAQ ID - 3941
My overall RNA yield is fine but RT-PCR performance poor – how can I improve this?
Use the standard protocol in order to allow for more efficient removal of crosslinks. This may improve RT-PCR performance but may also impact RNA integrity.
FAQ ID - 3945
Are there specific recommendations for performing RT-PCR on RNA isolated from paraffin-embedded samples?
Paraffin-embedded or fixed samples typically yield fragmented, partially degraded RNA. In addition, RNA quality will depend greatly on the handling of the samples before, during, and after the fixation procedure. 
If performing RT-PCR with degraded RNA, we recommend for cDNA synthesis the use of gene-specific primers or random nonamers rather than oligo-dT primers, since the mRNA poly-A tail may have been lost due to degradation. Regarding PCR primer design, shorter amplicon sizes are preferable.
FAQ ID - 3944
Are there other options for paraffin removal?
Deparaffinization with the supplied Paraffin Removal Solution is recommended, however, other standard methods such as heptane and methanol or xylene can be used as well.
QIAGEN’s Deparaffinization Solution (DPS), catalog number 939018, can be used for removal of paraffin. For this adhere to the following procedure:
1. Place the FFPE sections in a 1.5 ml or 2 ml microcentrifuge tube (not supplied). Add 300 μl Deparaffinization Solution, vortex vigorously for 10 s, and centrifuge briefly to bring the sample to the bottom of the tube.
2. Incubate at 56°C for 3 min, then allow to cool to room temperature.
Note: If too little Deparaffinization Solution is used or if too much paraffin is carried over with the sample, Deparaffinization Solution may become waxy or solid after cooling. If this occurs, add additional Deparaffinization Solution and repeat the incubation at 56°C.
After this, proceed with step 7 of the EZ2 preparation in the Quick Start Protocol for the EZ2 RNA FFPE Kit.
FAQ ID - 3946
Which version of the EZ2 Connect can run the EZ2 RNA FFPE Kit?
All versions of the EZ2 Connect (EZ2 Connect, EZ2 Connect Fx and EZ2 Connect MDx) can run the kit.
FAQ ID - 3940