Affymetrix Gene Expression Profiling Services
Asuragen performs hundreds of Affymetrix profiling jobs per month, and was the only
commercial service provider participating for the Affymetrix platform in the pivotal
MAQC study. Our
validated procedures and optimized processes give you the quality and turn-around
time critical for a successful experiment.
Learn more about how we qualify our methods and staff.
Description of Services – 3′ Expression and
Whole Transcript Array (WTA) processes
Workflow for all array services:
- Incoming total RNA QC (click here for
sample prep services):
- Quantitation and estimation of RNA purity using NanoDrop spectrophotometer readings at 260 and 280 nm
- Assessment of RNA integrity using Agilent 2100 Bioanalyzer to measure
RNA integrity number (RIN) for RNA prepared by Asuragen (not applicable for FFPE samples)
- See our
Sample Submission Form and
Shipping Instructions for recommended incoming sample QC values
- Target preparation, specific to the array/probe platform followed
by cRNA QC
- Array hybridization, washing, and scanning followed by array QC
- Data summarization (additional
analysis services)
Target preparation:
3′ Expression array service is available for many eukaryotic and prokaryotic genomes.
Whole Transcript Expression array service is available for human, rat, and mouse.
Utilizing the Affymetrix recommended single-round amplification process, the target
preparation process consists of reverse transcription (RT), second strand cDNA synthesis,
and IVT cRNA generation (eukaryotic only).
Asuragen’s unique low-mass Affymetrix service enables
single-round amplification with an optimized RT, second-strand cDNA synthesis, and
IVT cRNA process but requires only 100 ng of input RNA – twenty-fold less than
the standard Affymetrix process.
For even lower input amounts, Asuragen can provide double-round amplification. While
this method may introduce additional artifacts, it may be the preferred method for
total RNA amounts less than 10 ng.
Contact us about this and other alternative protocols available as a custom
molecular biology service.
Deliverables
Included in the price of gene expression profiling, you will receive:
- Affymetrix scanner outputs packaged in DTT format with an additional
copy of each CEL file packaged in a compressed format ready for import into your
analysis software
- Microsoft Excel® workbook containing:
- Gene Identifiers
- Summarization of RNA QC values
- Gene expression values that are summarized and normalized according
to a number of available options.
- Affymetrix Array QC Report
- Agilent Bioanalyzer RNA QC report in PDF format
To ensure security, all information is provided in an electronic form on a DVD.
Encryption is available on request. Data may also be delivered by FTP or e-mail.
Quality Control
During our processes, we monitor many QC checkpoints as recommended by the Affymetrix
GeneChip procedures. As much as possible, we utilize spike-in controls, in-process
sample controls, and process or reagent batch controls. Should any sample-specific
QC measure result in an “alert” or “fail” reading, we will contact you to discuss
available options. 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 projects 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.
Data Analysis
Asuragen’s bioinformatics team is very experienced with Affymetrix GeneChip analysis.
As part of the Standard Service for gene expression profiling, our team summarizes
the data and provides you with a report that outlines each step of the analysis
project and presents your findings so that you can advance to the next stage of
investigation and experimentation.
Additional Data Analysis
Standard Service Premium (SSP) For statistical analysis and graphical
representation of your entire experiment, our SSP data analysis package offers additional
analysis and these deliverables:
- Hypothesis testing by one- or multi-way ANOVA of the summarized
array data, providing p-value and fold-change information relevant to your
experimental groups
- Publication-quality figures and images, including:
- Hierarchical clustering
- Pair-wise volcano plot(s)
- Box plot(s)
- Principal components analysis (PCA) plot(s)
These are provided in electronic form on the data delivery DVD in addition to the
standard deliverables provided with every gene expression profiling project.
With all SSP projects we will call you upon shipment of your data to arrange a one-hour
web-based informatics review of your data.
Full Service
Based on your
initial consultation, Asuragen can define expert analysis for a custom informatics
approach. See our Informatics
section for more information on our capabilities.
Additional Services Available
Available GeneChip® Arrays:
3′ Expression Arrays
Whole Transcript Expression Arrays
Human Gene 1.0 ST Array
Human Exon 1.0 ST Array
Rat Gene 1.0 ST Array
Rat Exon 1.0 ST Array
Mouse Gene 1.0 ST Array
Mouse Exon 1.0 ST Array
Design your own custom arrays using Affymetrix CustomExpress Arrays. Please contact
Customer Support for more
details.
Other Microarrays
Made-to-Order
Arrays
CustomExpress®
Arrays
Test3 Array
Catalog Numbers for Gene Expression Services
|
CA0010
|
QC, NanoDrop and Bioanalyzer, Total RNA, for mRNA applications
|
|
CA0011
|
Target Preparation, cRNA, Affymetrix standard input with QC
|
|
CA0033
|
Target Preparation, cRNA, Affymetrix Low Mass Input with QC
|
|
CA0013
|
Target Preparation, cDNA, Affymetrix standard input with QC
|
|
CA0012
|
Array Processing and Scanning, Affymetrix Arrays Hybridization, Scanning, and Analysis
of Affymetrix Array
|
|
CC0010
|
Affymetrix Human Genome U133 Plus 2.0 Array*
|
*Asuragen supports a broad range of arrays from Affymetrix.
Contact Asuragen for more detail.
Requirements for Affymetrix Gene Expression Profiling Services
Sample input requirements for these and other services listed above are found in
the Sample Submission Form
and
Shipping Instructions.