Formalin-fixed paraffin-embedded (FFPE) tissues are widely used in clinical research and molecular diagnostics. However, formaldehyde fixation introduces crosslinking between nucleic acids and proteins, leading to fragmentation and reduced extraction efficiency.
Effective FFPE nucleic acid extraction requires optimized workflows for crosslink reversal, contaminant removal and recovery of fragmented DNA or RNA suitable for downstream applications such as PCR, qPCR and next-generation sequencing (NGS).
Magen provides a complete FFPE sample preparation system based on both silica membrane and magnetic bead technologies, supporting DNA extraction, RNA extraction and DNA/RNA co-extraction workflows across different experimental requirements.
This guide helps laboratories and distributors select appropriate FFPE extraction kits based on sample type, workflow preference and downstream application.
For a technical route-level overview of FFPE DNA, RNA and DNA/RNA co-extraction workflows, including early partition, sequential adsorption, fragment-selection DNA and DNase-integrated RNA workflows:
Selection can be based on target nucleic acid type, downstream application and nucleic acid quality requirements:
For Routine column workflows, refer to (HiPure FFPE DNA Kit, D3126) | View workflow
For NGS-oriented workflows, refer to (MagPure FFPE DNA Kit, D6323B) | View workflow
For High-purity requirement, refer to (MagPure FFPE DNA Kit (High Pure), D6323D) | View workflow
For Routine FFPE RNA extraction, refer to (HiPure FFPE RNA Kit, R4143) | View workflow
DNA-free FFPE RNA (column workflow) , refer to (HiPure FFPE RNA Plus Kit, R4144)
DNA-free FFPE RNA (magnetic workflow) ,refer to (MagPure FFPE RNA Kit, IVD3022) | View workflow
For high-recovery workflows, refer to (MagPure FFPE DNA/RNA Kit, R6327) | View workflow
For RNA integrity-sensitive workflows, refer to (MagPure FFPE DNA/RNA Kit, IVD3026) | View workflow
For Column-based workflows, refer to (HiPure FFPE DNA/RNA Kit, IVD5116) | View workflow
| Product | Technology | Nucleic Acid | Key Strategy | Best For |
|
HiPure FFPE DNA Kit (D3126) ⭐ |
Spin column | DNA | Silica membrane purification after FFPE lysis and crosslink reversal | Routine FFPE DNA extraction for PCR, genotyping and mutation detection |
|
MagPure FFPE DNA Kit (D6323B) |
Magnetic bead | DNA | Fragment-size selective purification | NGS library preparation and mutation profiling from FFPE DNA |
|
MagPure FFPE DNA Kit (High Pure) (D6323D） |
Magnetic bead | DNA | Dual binding purification chemistry | PCR, qPCR and inhibitor-sensitive molecular assays |
|
HiPure FFPE RNA Kit (R4143) |
Spin column | RNA | Silica column RNA purification | Routine FFPE RNA extraction for RT-PCR and gene expression analysis |
|
HiPure FFPE RNA Plus Kit (R4144) |
Spin column + DNase I |
RNA | Column purification with on-column DNase digestion | Reduced genomic DNA carryover in FFPE RNA preparation for qRT-PCR, gene expression analysis and DNA-sensitive downstream assays |
|
MagPure FFPE RNA Kit (IVD3022) |
Magnetic beads + DNase I |
RNA | Magnetic purification with DNase treatment | Automated FFPE RNA purification with DNase digestion for qRT-PCR, gene expression analysis and other DNA-sensitive RNA workflows |
|
HiPure FFPE DNA/RNA Kit (IVD5116) |
Spin column | DNA + RNA | DNA precipitates during lysis while RNA remains in supernatant, followed by separate column purification | Parallel DNA and RNA purification for PCR, real-time PCR and pyrosequencing |
|
MagPure FFPE DNA/RNA Kit (R6327) ⭐ |
Magnetic bead | DNA + RNA | Sequential magnetic adsorption | High-recovery DNA/RNA co-extraction, multi-omics studies and parallel DNA/RNA analysis |
|
MagPure FFPE DNA/RNA Kit (IVD3026) |
Magnetic bead | DNA + RNA | Early nucleic acid partition during digestion | RNA-focused FFPE DNA/RNA co-extraction, RNA exome sequencing and workflows prioritizing RNA integrity |
For detailed product specifications and workflow descriptions, please refer to individual product pages.
Magen FFPE extraction solutions are organized into three workflow categories: DNA extraction, RNA extraction and DNA/RNA co-extraction. Column-based systems provide stable and reproducible performance for routine laboratory workflows, while magnetic bead systems support flexible processing and automation.
Effective FFPE nucleic acid extractionrequires optimized workflows for crosslink reversal, contaminant removal andrecovery of fragmented DNA or RNA suitable for downstream applications such asPCR, qPCR and next-generation sequencing (NGS).
Within the system, core workflows are represented by the HiPure FFPE DNA Kit (D3126) and MagPure FFPE DNA/RNA Kit (R6327), while additional kits provide optimized solutions for specific applications such as RNA integrity preservation, fragment-size selection or high-purity DNA recovery.
This structured approach allows laboratories to select extraction workflows based on experimental priorities rather than adapting workflows to a single kit format.
