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:
- Asuragen-isolated RNA or DNA suitable for numerous downstream
applications, including expression profiling and genotyping studies (additional
services)
- RNA isolation methods optimized to recover miRNA
- Basic histology services also available
Workflow for FFPE sample prep:
- Accessioning of blocks, slides, or slices
- Optional slicing and H&E staining
- Pathology assessment by a staff board-certified pathologist
- Optional macrodissection
- De-paraffinization
- RNA (with miRNA fraction) or DNA extraction
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
gene expression services,
miRNA profiling services, or
genotyping 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 for FFPE
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 FFPE samples prepared by Asuragen
Services are routinely qualified by spectrophotometry with the NanoDrop spectrophotometer and gel electrophoresis (where
applicable). Due to the degraded nature of RNA/DNA from FFPE tissues, special quality
control measurements are used in place of the Bioanalyzer (used as QC metrics for
intact RNA). Regardless of downstream application, detailed QC reports including
nucleic acid concentration, electropherograms (where applicable), gel electrophoresis
(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/DNA, excluding the sample from
further analysis, or proceeding at-risk.
Electropherograms of (A) highly intact RNA and (B) partially 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
Most products are completed in one to two weeks. 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/DNA isolation to better estimate potential yield and enable correlation
with conventional pathology assessment.
While it is very difficult to predict yield from FFPE tissue with great accuracy,
Asuragen can provide guidance on 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
Applied
Biosystems TaqMan Gene Expression Services
miRNA Analysis:
Ambion/Affymetrix
DiscovArray miRNA Expression Profiling
Agilent miRNA Microarray Service
Applied
Biosystems TaqMan miRNA Expression Services
DNA Analysis:
Agilent
aCGH
Affymetrix SNP 6.0 - coming soon
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
|
CA0063
|
Sample Prep, Slicing FFPE Block, per sample (up to 5 slices or slides)
|
|
CA0064
|
Sample Prep, Descriptive pathology, per slide (includes H&E staining)
|
|
CA0076
|
Sample Prep, Macrodissection (up to 5 slides per sample)
|
|
CA0008
|
Isolation, Total RNA from FFPE (up to 4 slides or sections of up to 20 μm thickness)
|
|
CA0025
|
Isolation, DNA
|
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.