Affymetrix® Platform


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.

Services Available
Technology
Quality Control
Sample Handling and Processing
Turn-around Time
Related Services
Catalog Numbers for Affymetrix Services

Services Available

Technology

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 the gene.


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 users.


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 the Affymetrix NetAffx Website.

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) 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.


Yield:

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 tissue handling.

 
Integrity:

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 standardization.


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 submission form and instructions.


Turn-around Time

Typical turn-around time is two weeks or less. 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.


Related 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 Affymetrix Services

Gene Expression

CA0010 Initial QC Test ND-1000 and Bioanalyzer Assays
CA0011 cRNA Target Prep and QC:  Affymetrix Standard Input (for eukaryotic samples)
CA0033  cRNA Target Prep and QC:  Affymetrix Low Mass Input (for eukaryotic samples
CA0013  cDNA Target Preparation and QC (for prokaryotic samples)
CA0012  Hybridization, Scanning, and Analysis of Affymetrix Array
CC0010  Affymetrix Human Genome U133 Plus 2.0 Array


Gene Expression Data Analysis

CS0001 Fee, Initial Consult or Design Plan
CS0002 Data Analysis, mRNA, Standard Service Premium
CS0003  Fee, Setup


miRNA Expression

CA0010 QC, NanoDrop and Bioanalyzer, Total RNA, for Arrays
CA0039 Target Preparation, Affymetrix
CA0040 Target Preparation, miRNA, Affymetrix DiscovArray Process
CA0040 Array, Array Processing and Scanning, Affymetrix DiscovArray Process


miRNA Expression

CS0010 Data Analysis, Custom
CS0020 miRInform™ Data Delivery System for DiscovArray and Agilent miRNA Expression


*Asuragen supports a broad range of arrays from Affymetrix.  Contact Asuragen for more detail.