The perfect solution for FFPE sample nucleic acid (DNA/RNA) preparation

February 06 09:06:16, 2023

Archiving of formalin-fixed, paraffin-embedded (FFPE) tissue sections represents a valuable and widely sourced biomedical research material. As more and more researchers turn to molecular analysis of FFPE samples to develop specific operational steps, it is becoming increasingly important to consider the unique properties of these samples. QIAGEN offers a complete solution for the entire process of FFPE sample purification and downstream testing.
QIAamp DNA FFPE Tissue Kit - Purification of genomic DNA from paraffin-embedded tissues
Specially optimized lysis and reverse cross-linking Buffer to ensure efficient release of DNA
Quickly purify high quality, ready-to-use DNA from wax blocks in 30 minutes
Flexible elution volume: from 20 Î¼l to 100 Î¼l
A single sample size can be as high as 8 wax block samples
Automated purification on QIAcube

Genomic DNA was purified from different FFPE tissue samples using the QIAamp DNA FFPE Tissue Kit. Real-time quantitative PCR amplification of prnp gene (78 bp, 464 bp and 727 bp) products

Figure 1 PCR analysis of DNA purified from FFPE tissue samples.
RNeasy FFPE Kit - Purification of total RNA from paraffin-embedded tissues
Optimized cleavage and reverse cross-linking buffers ensure efficient release of RNA
Fast operation, purified RNA in 85 minutes
Contains DNase to ensure contamination without genomic DNA
Automated purification on QIAcube

After removing the paraffin from the sample, the enzyme cleavage was performed in the optimized lysis buffer, and the sample cleavage was completed in 15 minutes without affecting the RNA yield. After lysis, the samples were incubated at 80 Â°C for 15 minutes to reverse formalin cross-linking. The DNase and DNase Booster Buffer were then used to efficiently remove genomic DNA, including small DNA fragments from FFPE samples. Finally, the concentrated RNA was purified using an RNeasy MinElute spin column. The elution volume of RNA is only 14â€“30 Î¼l, thus reducing the volume of reaction in downstream operations.

Figure 2 RNeasy FFPE experimental procedure.
Total RNA was purified from rat kidneys using the RNeasy FFPE Kit. Real-time RT-PCR analysis of PGK1 (phosphoglycerate kinase 1) was performed on a Rotor-Gene Q real-time PCR analyzer using (+RT) or without (-RT) reverse transcriptase. The -RT curve demonstrates that RNA purified using the RNeasy FFPE Kit contains virtually no genomic DNA.
miRNeasy FFPE Kit - Purification of total RNA containing miRNA from paraffin-embedded tissues
Effective purification of miRNA and total RNA (see Figure 3)
Optimized cleavage and reverse cross-linking buffers ensure efficient release of RNA
Contains DNase to ensure contamination without genomic DNA
Figure 3 Successful real-time RT-PCR analysis from FFPE samples.
Rat liver tissue was fixed with formalin for 24 hours or 60 hours, and then total RNA including miRNA was purified using the miRNeasy FFPE Kit. Quantitative real-time RT-PCR analysis was performed using the miScript PCR System and purified RNA as a template to detect larger mRNAs of miRNA miR-16 and miR-29a and PGK1 genes. The results showed that both miRNAs and mRNAs were detected simultaneously from the same eluate.
Product List:
product name
Item number
QIAamp DNA FFPE Tissue Kit (50)
56404
RNeasy FFPE Mini Kit (50)
74404
miRNeasy FFPE Kit (50)
217504
QIAamp DSP DNA FFPE Tissue Kit (50)
60404
Deparaffinization Solution (16 ml)
19093

Figure 4 Efficient real-time RT-PCR.
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