HiPure FFPE RNA Plus Kit

HiPure FFPE RNA Plus Kit extends the standard FFPE RNA purification workflow by integrating DNase digestion during RNA extraction. Removal of genomic DNA contamination improves reliability of downstream transcription and gene expression analysis.

The workflow maintains the same column-based RNA purification chemistry while incorporating a dedicated cleanup step to improve RNA purity.

For standard RNA purification workflows see HiPure FFPE RNA Kit - R4143.

Laboratories requiring simultaneous DNA and RNA purification from the same FFPE tissue digestion may refer to MagPure FFPE DNA/RNA Kit - R6327.

Workflow

Workflow Overview

The HiPure FFPE RNA workflow uses a silica column–based route for purification of RNA from FFPE sections. Following deparaffinization, proteinase K digestion and controlled heat treatment, RNA binding conditions are established and RNA is purified through membrane binding, washing, drying and elution. An optional DNase treatment route is included when reduced genomic DNA carryover is required for downstream RNA analysis.

Sample Handling Logic

This workflow is designed for FFPE RNA recovery, where controlled heat exposure and residual DNA management are especially important. FFPE RNA is often fragmented before extraction begins, so the workflow balances tissue digestion and heat-assisted release with conditions intended to avoid unnecessary additional stress. When downstream assays are sensitive to genomic DNA contribution, the DNase treatment route provides an additional control point.

Time and Workflow Characteristics

Under typical manual operation, the overall workflow usually requires about 1~1.5 hours, depending on whether DNase treatment is included and on sample handling conditions. For detailed step-by-step conditions, workflow guidance and estimated processing times, please refer to the Workflow Note in the Download section.

Specifications

Principle

This product is based on silica column purification. Remove paraffin by Buffer DPS. Sample lysis with proteinase K digestion requires only 15 minutes. After lysis, samples are incubated at 80ºC for 15 minutes. Transfer to an adsorption column and RNA is adsorbed on the membrane, while protein is not adsorbed and is removed with filtration. After washing proteins and other impurities, RNA was finally eluted with low-salt buffer.

Technical Validation

HiPure FFPE RNA Kit was evaluated as a silica column-based RNA extraction workflow for formalin-fixed, paraffin-embedded tissue samples. The workflow includes deparaffinization, proteinase K digestion, 80°C heat treatment for reversal of formaldehyde-related modifications, and column-based RNA purification without phenol / chloroform extraction or alcohol precipitation.

In FFPE tissue testing, RNA was extracted from 9 mg paraffin-embedded tissue samples, including grass carp liver, grass carp muscle, chicken liver, and chicken heart. From 9 mg FFPE fish liver input, RNA yields were 14.8–22.9 µg. From 9 mg FFPE chicken liver input, RNA yields were 21.2–25.1 µg. Lower-yielding tissue types, including fish muscle and chicken heart, produced 1.5–1.7 µg and approximately 2.8 µg RNA, respectively, under the tested conditions.

Additional workflow testing showed that RNA integrity was maintained after the 80°C heat-treatment step used in the FFPE protocol. Using 200 µL cell input and 6 mg plant leaf input as model materials, RNA extracted after 55°C digestion followed by 80°C treatment showed clear electrophoresis band patterns, and the eluted RNA remained stable after overnight storage at 4°C before electrophoresis analysis.

In a paired comparison using six lung cancer FFPE samples, two tissue sections were processed per extraction with HiPure FFPE RNA Plus Kit and a leading commercial FFPE RNA extraction workflow. R4144 generated Qubit-measured RNA amounts of 2.8–18.1 µg in a 50 µL elution volume, compared with 1.53–15.8 µg from the reference workflow. Across the six paired samples, R4144 provided comparable or higher RNA recovery in most cases, with A260/280 and A260/230 values remaining in a comparable range. These results support R4144 for FFPE RNA extraction from clinical FFPE tissue sections where both RNA recovery and genomic DNA control are required.

Kit Contents

Storage and Stability

Proteinase K should be stored at 2–8°C upon arrival. DNase I should be stored at -20°C. However, short-term storage (DNase I up to 1 weeks, Proteinase K up to 8 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.

Experiment Data

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: