Asuragen is an experienced Affymetrix GeneChip® service laboratory and
was the only commercial service laboratory for the Affymetrix platform in the pivotal
2006 MAQC Study.
Affymetrix uses a novel photolithographic and solid phase chemistry to synthesize
25-base long oligonucleotides on its arrays. Each array contains about 1.3 million
different oligonucleotides. Each spot on the array contains millions of copies of
a single oligonucleotide (each spot is also called a “probe cell”). The generation
of a GeneChip array is a multiple step procedure. In the first step of the process,
a glass slide with linkers containing photolabile groups is generated. A mask applied
to the slide then determines the regions of the slide that will be exposed to ultraviolet
light. By applying ultraviolet light the photo-labile protecting groups are removed
from the exposed regions of the mask to allow addition of nucleoside phosphoramidites.
This step is repeated with different masks, and addition of subsequent nucleoside
phosphoramidites based on the sequence of the oligonucleotides being synthesized
in a given spot.
3′-based Expression Arrays
A wide range of arrays for over 30 eukaryotic and prokaryotic organisms are available
for analysis with 3′–based expression arrays. On these arrays, each gene is represented
by a set of 10-12 different oligonucleotide probe pairs. Each probe pair constitutes
a perfectly matched and a mismatched probe counterpart that is different at a single
base in the center of the probe. This design feature allows the demarcation between
signals obtained from specific binding vs. non-specific binding on the arrays. Most
of the probes on these expression arrays target unique sequences at the 3’ end of
Whole Transcript Expression Arrays
Whole Transcript and Alternative Splicing: Exon 1.0 ST Arrays
GeneChip Exon Arrays provide the most comprehensive coverage of the genome and enable
two complementary levels of analysis-gene expression and alternative splicing. Multiple
probes per exon enable “exon-level” analysis and allow you to distinguish between
different isoforms of a gene. This exon-level analysis on a whole-genome scale opens
the door to detecting specific alternative splicing events that may play a central
role in disease mechanism and etiology. You can also perform “gene-level” analysis,
in which multiple probes on different exons are summarized into a single expression
value of all transcripts from the same gene, enabling similar analysis workflows
to 3'-gene expression.
Whole Transcript: Gene 1.0 ST Arrays
The Gene 1.0 ST Array System offers a cost-effective solution for whole-genome,
whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated
genes is represented by approximately 26 probes spread across the full length of
the gene, providing a more complete and accurate picture of gene expression than
3'-based expression array designs. All 26 probes are automatically summarized into
a single expression value per gene, allowing standard analysis software packages
and simple analysis workflows to be used to analyze data. Gene 1.0 ST Arrays are
the most advanced and cost-effective gene expression profiling option for new microarray
Learn more about
Affymetrix Array Technologies
Asuragen utilizes the Affymetrix Integrated GeneChip System featuring the Hybridization
Oven 640 , the
Fluidics Station 450, the
GeneChip Scanner 3000 7G with autoloader, and the Affymetrix GeneChip
Operating System (GCOS) Software.
Affymetrix customers can access array content and annotation information through
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)
and electropherograms where applicable, and purity are provided on each sample.
For FFPE samples, concentration and QC pass/fail information is provided. If a sample
does not pass a recommended QC metric 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.
RNA yield is primarily dependent on the tissue type and mass (or volume) but is
often affected by disease status, chemical treatment, media, preservatives, and
RNA integrity is dependent on a wide range of factors in the precise handling of
biological materials from collection to RNA isolation. Elimination of the activity
of endogenous endo- or exo-nucleases is vital to preserving RNA integrity, and typically
depends on treatment with proper preservative or freezing upon tissue collection.
Asuragen’s 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
Sample Handling and Processing
All samples are received and entered into the analysis queue under a controlled
SOP to confirm package/sample integrity, appropriate shipping conditions (frozen
samples/dry ice, as appropriate), and individual confirmation of sample identity
against the shipping manifest and sample
Typical turn-around time is 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.
Team offers a broad range of analytical services to help you get the most information
from your data.
Catalog Numbers for Affymetrix Services
QC, Nanodrop and Bioanalyzer, Total RNA, for mRNA Applications
Target Preparation, cRNA, Affymetrix standard input with QC (for eukaryotic samples)
Target Preparation, cRNA, Affymetrix Low Mass Input with QC (for eukaryotic samples)
Target Preparation, cDNA, Affymetrix standard input with QC (for prokaryotic samples)
Array Processing and Scanning, Affymetrix 3' and Gene ST Arrays
Affymetrix Human Genome U133 Plus 2.0 Array
Gene Expression Data Analysis
Fee, Initial Consult or Design Plan
Data Analysis, mRNA, Standard Service Premium
miRNA Expression DiscovArray™ Service
QC, NanoDrop and TaqMan, Total RNA, for microRNA Applications
Target Preparation, DiscovArray Low Mass Input
Array Processing and Scanning, Affymetrix DiscovArray Service (INCLUDES COST OF
miRNA Expression Data Analysis
Data Analysis, Custom
miRInform™ Data Delivery System for DiscovArray and Agilent miRNA Expression
*Asuragen supports a broad range of arrays from Affymetrix.
Contact Asuragen for more detail.