Introduction
MagPure FFPE DNA/RNA Kit (IVD3026) provides a magnetic bead workflow for simultaneous purification of genomic DNA and RNA from formalin-fixed paraffin-embedded tissue samples, with process design emphasizing improved RNA integrity.
In this workflow, DNA and RNA fractions are partitioned during the digestion stage prior to magnetic bead purification. Early separation reduces RNA exposure to conditions that may contribute to degradation during extraction and supports recovery of RNA with improved integrity from FFPE tissues.
After nucleic acid partitioning, magnetic bead purification is applied to isolate DNA and RNA fractions, maintaining compatibility with standard molecular biology workflows.
For workflows prioritizing Higher total nucleic acid yield, laboratories may refer to MagPure FFPE DNA/RNA Kit – R6327, where DNA and RNA separation occurs during the magnetic adsorption stage.
Additional FFPE purification workflows include:
IVD3026 serves as the RNA integrity–focused magnetic workflow within the Magen FFPE extraction system.
Details
Workflow
Workflow Overview
FFPE DNA/RNA Co-isolation Workflow I is based on an early partition strategy for recovering DNA and RNA from the same FFPE input. After shared FFPE pretreatment, the workflow separates the RNA-containing supernatant from the DNA-containing pellet. The two fractions then enter separate downstream routes, allowing RNA-oriented handling and DNA-oriented processing to be managed independently before final purification by column or magnetic bead workflow, depending on the kit format.
Sample Handling Logic
The key feature of this route is the early separation of RNA and DNA fractions. The RNA-containing supernatant is removed from the digestion residue and handled under RNA-oriented conditions, while the DNA-containing pellet can undergo additional processing and stronger heat-assisted reversal before DNA purification. This strategy is especially useful when RNA preservation and same-sample DNA/RNA recovery are both important considerations.
Time and Workflow Characteristics
Under typical manual operation, the early-partition column route represented by IVD5116 usually requires about 4.5 hours, while the early-partition magnetic route represented by IVD3026 usually requires about 4.7 hours. A dual-output workflow is complete only after both the RNA and DNA paths have been processed. For detailed step-by-step handling logic and route-specific timing, please refer to the Workflow Note in the Download section.
Specifications
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Features
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Specifications
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Main FunctionsC
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Co-isolation total RNA and DNA from FFPE tissue
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Applications
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RT-PCR, cDNA synthesis, PCR and second-generation sequencing, etc.
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Purification method
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Polydisperse magnetic beads
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Purification technology
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Magnetic beads technology
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Process method
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Manual or automatic
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Adaptive instrument
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Nucleic acid extractor and pipetting workstation
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Sample type
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FFPE slice, FFPE puncture sample, embedded tissue
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Sample amount
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No more than six 10µm sections of 150 mm2 surface area or three 20µm sections of 150 mm2 surface area.
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Extraction Principle
Formalin fixation introduces crosslinks between nucleic acids and proteins, while paraffin embedding adds contaminants that complicate nucleic acid recovery from FFPE tissues. Efficient extraction therefore requires both enzymatic digestion and controlled nucleic acid separation.
In the MagPure FFPE DNA/RNA workflow (IVD3026), tissue sections are first deparaffinized and digested using Proteinase K to release nucleic acids from the FFPE matrix. During this stage, an optimized lysis chemistry promotes differential behavior of nucleic acids: RNA remains soluble in the lysate while genomic DNA forms a precipitated fraction.
Following centrifugation, the RNA-containing supernatant and DNA-containing pellet are processed independently. Each fraction undergoes magnetic bead adsorption under chaotropic binding conditions, allowing efficient purification of RNA and DNA through separate magnetic workflows.
This lysis-stage nucleic acid partitioning strategy differs from conventional extraction methods where DNA and RNA remain in the same lysate until adsorption. By separating nucleic acids early in the workflow, the system improves recovery of intact RNA while maintaining efficient purification of genomic DNA from FFPE samples.
Application Scenario Summary
FFPE DNA/RNA-compatible workflows are useful when limited archived tissue may need to support more than one molecular direction, or when the study design requires flexibility between DNA-based and RNA-based analysis. The selected examples below involve Magen FFPE DNA/RNA extraction formats, including IVD3026, R6327 and D6323R.
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Application Scenario
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Related Format
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Sample Source
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Downstream Research Use
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FFPE NSCLC RNA-NGS validation of non-canonical RET rearrangements for fusion diagnostics
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IVD3026
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FFPE tissue samples from RET-rearranged Chinese NSCLC patients
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Total RNA extraction for targeted RNA-NGS, functional RET fusion transcript confirmation, non-canonical fusion partner validation and comparison of NGS, FISH and IHC diagnostic methods
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Locally recurrent rectal cancer genomic profiling for Wnt pathway recurrence mechanism research
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R6327
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FFPE tissue blocks from primary rectal cancer, locally recurrent rectal cancer, non-recurrent rectal cancer and matched normal rectal tissue samples
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DNA extraction for whole-exome sequencing, mutation landscape comparison, LRRC-specific pathway enrichment and Wnt signaling pathway candidate gene analysis
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Advanced NSCLC tumor–ctDNA paired genomic profiling for immunochemotherapy stratification research
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D6323R
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Tumor-derived genomic DNA used as paired tissue reference in advanced NSCLC; tissue samples were paired with pretreatment ctDNA samples for WES analysis
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Tissue-based WES combined with plasma ctDNA 520-gene targeted NGS and low-pass WGS to support ctDNA-based genomic immune subtype analysis, tissue–blood comparison and PD-1 inhibitor benefit stratification research
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EGFR-mutant NSCLC tumor genomic profiling for neoadjuvant immunochemotherapy response and MRD research
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D6323R + D6323B
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Pre-treatment biopsy and post-treatment resected tumor samples from EGFR-mutant stage IIB–IIIB NSCLC patients
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Tumor tissue gDNA extraction for WES, baseline and post-treatment genomic feature analysis, tumor-informed MRD panel design and response / resistance mechanism research
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Note: The selected examples involve FFPE DNA/RNA-compatible extraction formats, but the downstream nucleic acid differs by study. Some workflows use FFPE RNA for fusion transcript validation, while others use DNA extracted with a DNA/RNA-compatible format for WES or tumor genomic profiling. These examples should not be described as DNA/RNA multi-omics unless both DNA and RNA are explicitly used in the same study.
Kit Contents
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Contents
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IVD3026
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Purification Times
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200 Preps
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MagBind Particles
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9.0 ml
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Proteinase K
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180 mg
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Protease Dissolve Buffer
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10 ml
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Buffer DPS
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150 ml
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Buffer FRL
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40 ml
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Buffer ATL
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40 ml
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Buffer AL
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80 ml
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Buffer BXW1*
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110 ml
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RNase Free Water
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30 ml
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Storage and Stability
Proteinase K and MagBind Particles should be stored at 2-8°C upon arrival. However, short-term storage (up to 24 weeks) at room temperature (15-25°C) does not affect their performance. The remaining kit components can be stored at room temperature (15-25°C) and are stable for at least 18 months under these conditions.
Purchase Guide
For guidance on selecting the most appropriate FFPE nucleic acid extraction system based on target analyte, workflow format and downstream application requirements:
👉 FFPE Nucleic Acid Extraction Purchase Guide
For a broader technical overview of FFPE DNA, RNA and DNA/RNA co-extraction workflow routes, processing logic and application-oriented route design:
👉 FFPE Nucleic Acid Extraction Workflows Explained
For detailed workflow structure, estimated processing time and route-specific handling logic across representative FFPE workflows:
