RNA Extraction from FFPE Tissues: Overcoming Challenges and Ensuring Quality

Formalin-fixed paraffin-embedded (FFPE) tissues represent a vast archive of clinical material, yet extracting RNA from them requires specific protocols that address formalin-induced crosslinking and fragmentation. This article provides laboratory students, technicians, researchers, and diagnostic professionals with a practical framework for selecting extraction methods, assessing RNA quality, and troubleshooting common failures when working with archival FFPE specimens.

Nucleic acid isolation is often the starting point for all downstream experiments in biomedical research, making it the most crucial step in any molecular technique [6]. DNA and RNA extraction follow protocols with standardized reagents, many of which are available in quality-controlled commercial kits [6]. Irrespective of the protocol, successful extraction of high-quality nucleic acid from biological tissues requires sufficient disruption of the tissue and cellular structures, denaturation of nucleoprotein complexes, inactivation of nucleases, and nucleic acid purification [6]. These steps can be modified based on the nucleic acid of interest and the biological sample source [6].

The Unique Challenges of FFPE RNA

FFPE tissues are heavily fragmented and chemically cross-linked by formalin due to the harsh nature of fixation and embedding procedures involved in preserving clinical material [7]. This presents fundamental obstacles for RNA work that do not apply to fresh or frozen specimens.

Formalin Crosslinking and RNA Fragmentation

Formalin fixation creates methylene bridges between nucleic acids and proteins, trapping RNA in a crosslinked matrix. The same chemical processes that preserve tissue morphology degrade RNA over time. Archived FFPE samples represent a valuable resource for the determination of gene expression for physiopathological conditions, but the quality and quantity of recoverable RNA depend heavily on pre-analytical variables [8].

Genome-wide gene expression profiling analysis of FFPE tissue samples is indispensable for cancer research and provides the opportunity to evaluate links between molecular and clinical information, however, working with FFPE samples is challenging due to extensive cross-linking, fragmentation, and limited quantities of nucleic acid [9]. These factors mean that standard RNA extraction protocols designed for fresh tissue often fail when applied to FFPE material.

Storage Time Effects

Storage time significantly impacts RNA quality in FFPE blocks. In a study of thyroid cancer patients, the median storage time was significantly longer in the case of inadequate samples for RNA-based next-generation sequencing compared with adequate specimens, with samples archived for three years or more leading more frequently to an inadequate result [16]. RNA quality showed a negative correlation with RNA integrity number and a positive correlation with threshold cycle as archiving time increased, although RNA from samples as old as 10 years showed a 100% success rate in quantitative real-time PCR using short primers, demonstrating that the effect of archiving time can be overcome by proper experiment design [21].

Tissue Processing History

Pre-analytical handling before fixation matters as much as storage duration. Specimens that were stored in a refrigerator for more than six hours and fixed without slicing showed lower success rates and worse results than specimens from institutions with better processing workflows [21]. Archived FFPE tissues can be used to extract RNA for next-generation sequencing if they are properly processed before fixation [21].

Core Principles of FFPE RNA Extraction

Successful RNA extraction from FFPE tissue requires addressing four interconnected challenges: removing paraffin, reversing formalin crosslinks, inactivating nucleases, and purifying fragmented RNA from contaminants.

Deparaffinization

Paraffin must be completely removed before lysis because residual paraffin interferes with downstream enzymatic reactions. A modified deparaffinization protocol conducted prior to RNA isolation improved results compared with standard approaches [9]. Deparaffinization can be achieved through organic solvent extraction or through heat-based methods that melt paraffin into an aqueous phase.

Proteinase K Digestion

Proteinase K digestion is critical for releasing RNA from the crosslinked protein matrix. It is critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA in dual extraction protocols [12]. Insufficient digestion leaves RNA trapped, while excessive digestion can degrade already fragile RNA.

Crosslink Reversal

Heat treatment during extraction helps reverse formalin crosslinks. The specific temperature and duration vary by kit protocol, and following manufacturer instructions precisely is essential because over-treatment can fragment RNA further.

Purification

RNA purification removes proteins, genomic DNA, and inhibitors that interfere with downstream applications. Most commercial kits use silica-based column binding or magnetic bead capture. The choice of purification chemistry affects also yield but also the quality metrics used to assess RNA suitability for downstream applications [25].

At a Glance: FFPE RNA Extraction Considerations

Selecting an RNA Extraction Kit

Multiple commercial kits are available for FFPE RNA extraction, and comparative studies provide guidance for kit selection based on specific research needs.

Comparative Kit Performance

A systematic comparison of seven commercially available RNA extraction kits for renal tissue found that total RNA can be extracted from archival renal biopsies in sufficient quality and quantity from one human kidney biopsy section and from around 100 laser capture microdissected glomerular cross-sections to enable successful RNA library preparation and sequencing [13]. The kits evaluated included High Pure FFPE RNA Isolation from Roche, ExpressArt Clear FFPE RNAready from Amsbio, miRNeasy FFPE and RNeasy FFPE from Qiagen, PureLink FFPE Total RNA from Invitrogen, RecoverAll Total Nucleic Acid Isolation from Ambion, and Absolutely RNA FFPE Kit from Agilent [13].

For miRNA extraction specifically, the Qiagen miRNeasy FFPE kit was determined to be the best kit for this task [7]. miRNAs, due to their small size and increased stability, are easier to retrieve and study in FFPE tissues [7].

Method-Specific Outcomes

A comparison of three different RNA extraction methods on diffuse large B-cell lymphoma specimens found that RNA extraction methodology impacts both preanalytical and sequencing-based gene expression results [25]. Two silica-based procedures and one isotachophoresis-based procedure were evaluated, with the isotachophoresis-based method and one silica-based method outperforming the other silica-based method by showing significantly higher fractions of uniquely mapped reads, an increased number of detectable genes, a lower fraction of duplicated reads, and better representation of the B-cell receptor repertoire [25]. Differences among the extraction methods were generally more explicit for total RNA sequencing than for exome-capture sequencing [25]. Importantly, the predictive value of quality metrics varies among extraction kits, and caution should be applied when comparing and interpreting results obtained using different kits [25].

Protocol Modifications

Optimizing protocols can yield higher-quality RNA. In a study of cardiac tissue specimens, four RNA extraction methods were compared: the Qiagen AllPrep DNA/RNA method, the same method with a protocol modification on the ethanol wash step after deparaffinization, a CELLDATA RNA extraction method, and the CELLDATA method with protocol modifications on the lysis step [26]. The modified Qiagen method produced the highest RNA yield, while the modified CELLDATA method produced more extracts with DV200 values above 30% compared with other methods [26]. RNA extracts from the modified Qiagen method, characterized by high RNA yield, achieved sequencing results comparable to those from the modified CELLDATA method, characterized by high DV200 values [26].

Dual DNA and RNA Extraction

Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging [12]. The Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues, generating a median of 1475 ng DNA and 1786 ng RNA per sample [12]. The median DNA integrity number was 3.8 and the median DV200 for RNA was 33.2 [12]. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by quantitative PCR and 92% generated data deemed high quality [12]. Of the 130 RNA samples with DV200 of at least 20% used in RNA sequencing, all but 5 generated usable transcriptomic data with a mapping rate of at least 60% [12].

Practical Workflow for FFPE RNA Extraction

The following workflow represents a synthesis of evidence-based practices for FFPE RNA extraction.

Step 1: Specimen Assessment and Selection

Before beginning extraction, assess the specimen characteristics. Tissue punches taken from tumor-enriched regions provided the most reliable output in a large epidemiologic study [12]. The expected RNA amount per unit area is approximately 33 ng per square millimeter based on analysis of tumor cellularity [21]. This calculation is useful for determining how much tissue to use for downstream applications.

For small biopsies and cytologic specimens, pre-analytical factors such as details of specimen collection, processing, and storage workflow influence also RNA sequencing success rates but also the quality and accuracy of sequencing results [15]. Minimally invasive specimens are associated with a unique set of pre-analytical challenges owing to their small size, limited RNA yield, and distinct workflows [15].

Step 2: Deparaffinization

Remove paraffin using the method specified by your chosen kit. Modified deparaffinization protocols can improve RNA quantity and quality compared with standard approaches [9]. Ensure complete paraffin removal because residual paraffin inhibits downstream enzymatic reactions.

Step 3: Lysis and Proteinase K Digestion

Adjust proteinase K digestion time based on tissue volume to achieve balanced yields [12]. Larger tissue pieces require longer digestion. Insufficient digestion results in low yield, while excessive digestion can degrade RNA.

Step 4: Crosslink Reversal and Binding

Apply heat to reverse formalin crosslinks according to kit specifications. Bind RNA to the purification matrix under conditions that favor RNA retention.

Step 5: Washing and Elution

Wash to remove contaminants, then elute in a small volume of nuclease-free water or elution buffer. The elution volume affects final concentration and should be chosen based on downstream requirements.

Step 6: Quality Assessment

Assess RNA quantity and quality using appropriate methods. RNA quality is reflected by DV200 values, which represent the percentage of RNA fragments longer than 200 nucleotides, utilizing the Agilent 2100 BioAnalyzer [13]. RNA concentrations and cycle threshold values for housekeeping genes in FFPE samples were significantly correlated, indicating that quantitative PCR can serve as a functional quality check [8].

Quality Assessment Metrics for FFPE RNA

Traditional RNA quality metrics developed for fresh or frozen tissue do not translate directly to FFPE-derived RNA.

RNA Integrity Number Limitations

The average RNA integrity number for FFPE samples was 2.3 with a standard deviation of 0.9 in one study, and 84% of samples had RNA fragments longer than 200 nucleotides [8]. These low RIN values reflect the fragmented nature of FFPE RNA but do not necessarily predict failure in downstream applications.

DV200 as the Preferred Metric

DV200, the percentage of RNA fragments longer than 200 nucleotides, has become the standard quality metric for FFPE RNA. In a large epidemiologic study, RNA samples with DV200 of at least 20% used in RNA sequencing all but 5 generated usable transcriptomic data with a mapping rate of at least 60% [12]. The median DV200 for RNA was 33.2 in this study [12].

Yield Considerations

The median RNA concentration recovered from FFPE samples was 316.8 ng per cubic millimeter of tissue, ranging between 61.6 and 917.4 ng per cubic millimeter [8]. RNA was extracted from 150 specimens with an average yield of 401.8 ng per square centimeter of tissue in another study [10].

Quality Metric Interpretation

The predictive value of quality metrics varies among extraction kits, and caution should be applied when comparing and interpreting results obtained using different kits [25]. This means that a DV200 threshold established with one kit may not apply directly to RNA extracted with a different kit.

Downstream Application Considerations

The intended downstream application should drive both extraction method selection and quality assessment strategy.

Whole Transcriptome Sequencing

Whole transcriptome sequencing is a ubiquitous tool for investigating cancer biology, and RNA isolated from frozen sources limits possible studies for analysis of associations with phenotypes or clinical variables requiring long-term follow-up [10]. Although good correlations are reported in RNA sequencing data from paired frozen and FFPE samples, uncertainties regarding RNA quality, methods of extraction, and data reliability are hurdles to utilization of archival samples [10].

Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from whole transcriptome sequencing between matched fresh frozen and FFPE samples, with median concordance correlation coefficients of 0.63 to 0.66 [11]. More than half of genes were differentially expressed between fresh frozen and FFPE, but with low fold change [11].

Targeted RNA Sequencing

Targeted RNA sequencing for a limited set of transcripts may tolerate lower quality RNA than whole transcriptome approaches. Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used [11].

Quantitative PCR

RNA from samples as old as 10 years showed a 100% success rate in quantitative real-time PCR using short primers, showing that the effect of archiving time can be overcome by proper experiment design [21]. Short amplicon designs are essential for work with FFPE RNA.

Spatial Transcriptomics

FFPE tissues are indispensable for clinical pathological assessment, yet widespread nucleic acid degradation severely hinders high-throughput molecular profiling [14]. Current RNA sequencing and in situ hybridization approaches for FFPE materials suffer from inconsistent performance across tissue types and preservation conditions [14]. Spatial transcriptomic technologies address the limitation of single-cell RNA sequencing by integrating high-resolution gene expression profiling with the preservation of native tissue architecture [20].

Common Failure Patterns and Troubleshooting

Understanding typical failure modes helps laboratories diagnose and correct problems efficiently.

Low RNA Yield

Low yield can result from insufficient tissue input, incomplete deparaffinization, inadequate proteinase K digestion, or loss during purification. Adjust proteinase K digestion time based on tissue volume to achieve balanced yields [12]. Tissue punches taken from tumor-enriched regions provided the most reliable output [12].

Degraded RNA

RNA degradation in FFPE tissue is expected due to the nature of fixation. However, excessive degradation beyond what is typical for the specimen age may indicate problems with tissue processing before fixation. Specimens stored for more than six hours before fixation showed lower success rates and worse results [21].

Inhibitors in Eluted RNA

Residual paraffin, proteins, or other contaminants can inhibit downstream enzymatic reactions. RNA purity is reflected by the 260/280 and 260/230 absorbance ratios [25]. If inhibitors are suspected, additional purification steps may be necessary.

Inconsistent Results Between Kits

Different extraction methods produce RNA with different quality profiles, and the predictive value of quality metrics varies among extraction kits [25]. If results are inconsistent, standardize on a single kit and protocol instead of switching between methods.

Sequencing Failures

RNA-based next-generation sequencing fails more frequently than DNA-based sequencing from the same specimens. Tissue samples were more frequently adequate for DNA-based next-generation sequencing compared with RNA-based next-generation sequencing, with adequacy rates of 93.9% versus 58.3% in one study [16].

Records and Documentation

Maintaining detailed records of FFPE RNA extraction supports quality assurance and troubleshooting.

Specimen Metadata

Record the following for each specimen: tissue type, collection date, fixation method and duration, processing date, block storage conditions, and block age at extraction. Storage time, defined as the interval between tissue collection and molecular testing, significantly impacts RNA quality [16].

Extraction Records

Document the kit and lot number, protocol version, tissue input amount, proteinase K digestion time, elution volume, and any protocol modifications. Protocol modifications can significantly affect outcomes, as demonstrated by improved DV200 values with modified lysis or wash steps [26].

Quality Metrics

Record RNA concentration, DV200, and any other quality metrics obtained. The median DNA integrity number was 3.8 and the median DV200 for RNA was 33.2 in a large study [12]. These values provide reference points for evaluating your own results.

Downstream Performance

Track the relationship between extraction quality metrics and downstream assay performance. RNA concentrations and cycle threshold values for housekeeping genes in FFPE samples were significantly correlated [8]. Expression patterns of normalized genes in paired FFPE and RNAlater preserved samples were significantly correlated, demonstrating that FFPE-derived RNA can produce biologically meaningful results [8].

Biosafety Considerations

Working with FFPE tissues requires attention to laboratory safety practices.

Chemical Hazards

Deparaffinization solvents and other extraction reagents present chemical hazards. Follow the Laboratory Biosafety Manual from the World Health Organization for guidance on safe handling of chemicals and biological materials [2].

Biological Hazards

FFPE tissues may contain infectious agents that survive fixation. Treat all specimens as potentially infectious and follow appropriate biosafety practices [2].

Quality Management

Laboratory quality management systems support reliable testing. The World Health Organization Laboratory Quality Management System Handbook provides guidance for establishing and maintaining quality systems in laboratories [1].

Professional Escalation Criteria

Laboratory personnel should know when to escalate problems to supervisors or seek additional expertise.

Escalate When Quality Metrics Fall Below Thresholds

If DV200 values consistently fall below the threshold required for your downstream application, escalate to determine whether protocol adjustments or alternative approaches are needed. RNA samples with DV200 of at least 20% used in RNA sequencing all but 5 generated usable transcriptomic data [12].

Escalate When Results Are Inconsistent

If the same specimen processed with the same protocol yields inconsistent results across runs, escalate to investigate potential causes including reagent lot variations, equipment malfunction, or technician technique differences.

Escalate When Downstream Assays Fail

If RNA sequencing or other downstream assays fail repeatedly despite acceptable quality metrics, escalate to review the entire workflow from specimen collection through data analysis. Pre-analytical factors influence also RNA sequencing success rates but also the quality and accuracy of sequencing results [15].

Escalate for Protocol Selection

When selecting a new extraction kit or protocol, escalate to involve appropriate expertise. The choice of extraction method impacts quality metrics and sequencing results [25]. Comparative studies provide evidence to support kit selection [13][25][26][27][28][29].

Limitations of FFPE RNA Analysis

Understanding the limitations of FFPE RNA analysis prevents overinterpretation of results.

Fragmentation Limits Assay Options

The fragmented nature of FFPE RNA limits the types of assays that can be performed successfully. Assays requiring long intact RNA molecules will fail with FFPE-derived RNA.

Crosslinking May Bias Results

Formalin crosslinking can bias recovery of certain RNA species. miRNAs, due to their small size and increased stability, are easier to retrieve and study in FFPE tissues [7].

Storage Time Effects Cannot Be Fully Reversed

While proper extraction methods can overcome some effects of storage time, samples archived for extended periods are more likely to yield inadequate results [16]. Samples archived for three years or more led more frequently to an inadequate result in RNA-based next-generation sequencing [16].

Quality Metrics Have Limitations

Quality metrics such as DV200 provide useful information but do not guarantee downstream success. The predictive value of quality metrics varies among extraction kits [25]. RNA extracts with high yield achieved sequencing results comparable to those with high DV200 values [26].

Frequently Asked Questions

Why is RNA from FFPE tissues so degraded compared with fresh tissue?

Formalin fixation creates chemical crosslinks between nucleic acids and proteins, and the same processes that preserve tissue morphology degrade RNA over time. FFPE samples are heavily fragmented and chemically cross-linked by formalin due to the harsh nature of fixation and embedding procedures [7]. The extent of degradation depends on factors including fixation conditions, storage duration, and tissue type.

What is DV200 and why is it preferred over RNA integrity number for FFPE RNA?

DV200 represents the percentage of RNA fragments longer than 200 nucleotides, as measured by capillary electrophoresis [13]. RNA integrity number is designed for intact RNA from fresh or frozen tissue and is less informative for the fragmented RNA typical of FFPE specimens. The average RNA integrity number for FFPE samples was 2.3 with a standard deviation of 0.9 in one study, while 84% of samples had RNA fragments longer than 200 nucleotides [8].

Which RNA extraction kit is best for FFPE tissues?

No single kit is universally best. Comparative studies show that different kits perform differently depending on tissue type and downstream application. The Qiagen miRNeasy FFPE kit was determined to be the best kit for miRNA extraction [7]. The Qiagen RNeasy FFPE kit with a modified deparaffinization step gave better results than other isolation kits in one comparison [9]. A systematic comparison of seven kits found that total RNA can be extracted from archival renal biopsies in sufficient quality and quantity using commercially available kits [13].

How much FFPE tissue is needed for RNA extraction?

The expected RNA amount per unit area is approximately 33 ng per square millimeter based on analysis of tumor cellularity [21]. The median RNA concentration recovered from FFPE samples was 316.8 ng per cubic millimeter of tissue [8]. RNA was extracted from 150 specimens with an average yield of 401.8 ng per square centimeter of tissue [10]. The amount needed depends on the downstream application and its input requirements.

Can RNA be extracted from very old FFPE blocks?

Yes, but success rates decline with storage time. RNA from samples as old as 10 years showed a 100% success rate in quantitative real-time PCR using short primers [21]. However, samples archived for three years or more led more frequently to an inadequate result in RNA-based next-generation sequencing [16]. The median storage time was significantly longer in the case of inadequate samples compared with adequate specimens [16].

How does the RNA extraction method affect sequencing results?

RNA extraction methodology impacts both preanalytical and sequencing-based gene expression results [25]. Different methods showed significantly different fractions of uniquely mapped reads, numbers of detectable genes, fractions of duplicated reads, and representation of specific gene repertoires [25]. The predictive value of quality metrics varies among extraction kits, so results obtained with different kits should be compared with caution [25].

Can DNA and RNA be extracted simultaneously from the same FFPE specimen?

Yes, dual extraction is feasible. The Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues, generating a median of 1475 ng DNA and 1786 ng RNA per sample [12]. It is critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA [12].

What quality metrics should be recorded for FFPE RNA extraction?

Record RNA concentration, DV200, and absorbance ratios where applicable. RNA quality is reflected by DV200 values utilizing the Agilent 2100 BioAnalyzer [13]. RNA purity is reflected by the 260/280 and 260/230 absorbance ratios [25]. Track downstream assay performance to establish the relationship between quality metrics and successful outcomes in your specific workflow.

Related Diagnostic Guides

• RNA Extraction from FFPE Tissues: Challenges and Protocols
• DNA Extraction from FFPE Tissues: Protocols and Quality Considerations
• RNA Extraction from Plant Tissues: Methods and Troubleshooting
• Genomic DNA Extraction from Blood: Protocols and Quality Assessment
• RNA Extraction Using TRIzol Reagent: Protocol, Troubleshooting, and Best Practices

References and Further Reading

• Laboratory Quality Management System Handbook. World Health Organization.
• Laboratory Biosafety Manual. World Health Organization.
• Assay Guidance Manual. National Center for Advancing Translational Sciences.
• Bioanalytical Method Validation Guidance. U.S. Food and Drug Administration.
• NCBI Literature Resources. National Center for Biotechnology Information.
• Nucleic Acid Extraction from Human Biological Samples.. Methods in molecular biology (Clifton, N.J.), 2019.
• Extraction of miRNAs from Formalin-Fixed Paraffin-Embedded (FFPE) Tissues.. Methods in molecular biology (Clifton, N.J.), 2017.
• Extraction of RNA from formalin-fixed, paraffin-embedded equine placenta.. Reproduction in domestic animals = Zuchthygiene, 2019.
• From RNA isolation to microarray analysis: Comparison of methods in FFPE tissues.. Pathology, research and practice, 2016.
• Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research.. bioRxiv : the preprint server for biology, 2024.
• The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues.. BMC cancer, 2019.
• Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study.. BMC genomics, 2022.
• RNA extraction for RNA sequencing of archival renal tissues.. Scandinavian journal of clinical and laboratory investigation, 2016.
• Automated in situ microfluidic Random-seq for robust single-nucleus and spatial total RNA profiling of diverse FFPE specimens.. 2026.
• Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.. 2026.
• Next-Generation Sequencing in Differentiated Thyroid Cancer Patients Treated with Lenvatinib: Results and Challenges in Real-Life Practice.. 2026.
• Comprehensive Genomic Profiling for Precision Oncology: Analytical Validation and Clinical Utility in Solid Tumors.. 2026.
• Spatial omics in high-grade glioma: study design, analytical pitfalls, and standards for reproducible neuro-oncology.. 2026.
• Single-Cell and Spatial Transcriptomics Reveal That &lt,i&gt,TXNIP&lt,/i&gt, and &lt,i&gt,BIRC3&lt,/i&gt, Contribute to Human Prostate Tumor Progression.. 2026.
• Spatial Transcriptomics of Early Tooth Morphogenesis in Formalin-fixed Paraffin-embedded Mouse Embryonic Tissue.. 2026.
• Optimization of RNA Extraction from Formalin-Fixed Paraffin-Embedded Blocks for Targeted Next-Generation Sequencing. Journal of Breast Cancer, 2017.
• Simultaneously DNA and RNA Extraction from Formalin-Fixed Paraffin Embedded (FFPE) Tissue.. Journal of Biomolecular Techniques, 2019.
• Evidence-Based Practices DNA AND RNA EXTRACTION FROM FORMALIN-FIXED , PARAFFIN-EMBEDDED TISSUE BIOSPECIMENS. 2018.
• Extraction, Purification, and Next-Generation Sequencing (NGS) Analysis of DNA and RNA from Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue.. Methods in molecular biology, 2025.
• RNA Extraction Method Impacts Quality Metrics and Sequencing Results in Formalin-Fixed, Paraffin-Embedded Tissue Samples.. Laboratory investigation, a journal of technical methods and pathology, 2023.
• Optimizing RNA extraction methods for high-throughput transcriptome sequencing of formalin-fixed paraffin-embedded cardiac tissue specimens. PLoS ONE, 2024.
• Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits. Journal of Translational Medicine, 2025.
• Commercially available kits for manual and automatic extraction of nucleic acids from formalin-fixed, paraffin-embedded (FFPE) tissues. Acta Dermatovenerologica Alpina Pannonica Et Adriatica, 2015.
• Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores. Plos One, 2017.
• Optimizing RNA extraction and library preparation from oral squamous cell carcinoma FFPE sample s for next-generation RNA sequencing. Biomedical Research and Therapy, 2023.

This article is educational and does not replace validated laboratory procedures, institutional biosafety review, manufacturer instructions, or professional interpretation.