Sample Preparation and Isolation of RNA or DNA
Formalin-fixed, Paraffin-embedded (FFPE) tissues
Formalin-fixed, paraffin-embedded (FFPE) tissue samples can be a rich resource for retrospective discovery studies because large numbers of samples with clinical outcome data can be rapidly acquired and analyzed. However, the RNA degradation and sample variability typical of FFPE samples present challenges for gene expression studies. Although FFPE-derived RNA is not suited to all downstream applications, Asuragen scientists have now optimized the methods required to achieve high quality microarray and qRT-PCR data from this important resource, and routinely obtain valuable data for our own in-house research and development and for external service customers. Learn more about how we qualify our methods and staff.
Not all tissues are equal. Consult with our experts to discuss your tissue types, tissue processing, and any downstream applications to obtain a better understanding of the amount of tissues required for your experimental design.
Description of Services
Features of the FFPE sample prep services:
- All RNA isolation methods optimized to recover miRNA
- Methods may utilize exogenous DNA or RNA spiked-in controls
- Asuragen-isolated RNA or DNA suitable for numerous downstream applications, including expression profiling and genotyping studies (click here for additional services)
- Basic histology services also available
Workflow for FFPE sample prep:
- Accessioning of blocks, slides, or slices
- Optional slicing and H&E staining
- Optional macrodissection
- De-paraffinization
- Prep QC based on the spike-in control
Deliverables
Nucleic acid concentration and QC pass/fail information is provided for FFPE samples. Purified nucleic acid samples are shipped back to you on dry ice. Asuragen ships samples Monday through Wednesday and will notify you upon shipment.
Isolation services are often utilized with Asuragen’s molecular profiling services. Surplus RNA or DNA will be discarded unless otherwise requested. Additional shipping charges may apply for the return of residual blocks, RNA, or DNA.
Quality Control
No matter how robust the downstream processes, good data is dependent on sample quality; consequently, accurate measurement of sample quality is essential before deciding if a sample merits further analysis. All samples prepared by Asuragen Services are routinely qualified by spectrophotometry with the NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer. Due to the degraded nature of RNA from FFPE tissues, special quality control measurements are used in place of the Bioanalyzer. Regardless of downstream application, detailed QC reports including nucleic acid concentration, RNA integrity (RIN), electropherograms (where applicable), and purity are provided on each sample. For FFPE samples, concentration and QC pass/fail information is provided. If you have chosen to use Asuragen Services for additional services and a sample does not pass the recommended QC metrics for analysis, you will be contacted promptly to discuss possible solutions. These may include replacing the sample or re-isolating the RNA, excluding the sample from further analysis, or proceeding at-risk.
Electropherograms of (A) highly intact RNA and (B) degraded RNA typical of FFPE tissues.
These rigorous procedures enable Asuragen to be the only service provider to offer a Data Quality Guarantee:
- If, for any reason, a qualified sample does not pass our process control specifications, we will re-run the sample at no additional charge.
Read more about our commitment to the best possible data quality, or read about our contributions to in-process controls and standardization.
Turn-around Time
If you have a critical time requirement, we can often meet your need for no additional charge. Read more about our commitment to prompt turn-around times
Typical Yields
Asuragen recommends characterizing the tissue area and histology adjacent the slices sent for RNA isolation to better estimate potential RNA yield and enable correlation with conventional pathology assessment.
While it is very difficult to predict RNA yield from FFPE tissue with great accuracy, Asuragen can provide guidance on RNA yield per tissue volume (area x thickness) for a wide array of common human tissues.
Additional Services Available
mRNA Analysis:
Affymetrix Gene Expression Profiling Service
Illumina Gene Expression Profiling Services
miRNA Analysis:
Ambion/Affymetrix DiscovArray miRNA Expression Profiling
Agilent Human miRNA Microarray Service
Applied Biosystems TaqMan miRNA Expression Services
DNA Analysis:
Applied Biosystems TaqMan Gene Expression or SNP Detection Services
Data Analysis:
Asuragen’s Informatics Team offers a broad range of analytical services to help you get the most information from your data.
Catalog Numbers for Formalin-fixed, Paraffin-embedded (FFPE) Tissues Sample PrepServices
| CA0008 | Isolation, Total RNA from FFPE (up to 4 slides or sections of up to 20 μm thickness) |
| CA0025 | Isolation, DNA |
| CA0032 | QC, NanoDrop and TaqMan, Total RNA, for microRNA Applications |
Requirements for FFPE Sample Prep and Related Services
Sample Input Requirements for the services listed above are found in the Sample Submission Form and Shipping Instructions.