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
Deliverables
Quality Control
Turn-around Time
Data Analysis
Additional Services Available
Available GeneChip® arrays
Catalog Numbers for Affymetrix Services

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)

    • 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 (click here for 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.


Sample Submission Form and Shipping Instructions



Deliverables

Included in the price of gene expression profiling, you will receive:

  1. 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

  2. Microsoft Excel® workbook containing:

    1. Gene Identifiers

    2. Summarization of RNA QC values

    3. Summarization of gene values using MAS 5.0, with all arrays scaled to 500 using Affymetrix GeneChip Operating Software

    4. Affymetrix Array QC Report from Affymetrix Quality Reporter

  3. 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 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.


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

Animals Plants
Bovine Genome Array
C. elegans Genome Array
Canine Genome Array
Chicken Genome Array
Drosophila Genome Arrays
Human Genome Arrays
Mouse Genome Arrays
Plasmodium/Anopheles Genome Array
Porcine Genome Array
Rat Genome Arrays
Rhesus Macaque Genome Array
Zebrafish Genome Array 		Arabidopsis Genome Arrays
Barley Genome Array
Maize Genome Arrays
Medicago Genome Arrays
Rice Genome Array
Soybean Genome Array
Sugar Cane Genome Array
Tomato Genome Array
Vitis vinifera (Grape) Array
Wheat Genome Array

Xenopus laevis Genome Array

Yeast
Bacteria
Yeast Genome Arrays B. subtilis Genome Array
E. coli Genome Arrays
P. aeruginosa Genome Array
S. aureus Genome Array

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
CA0010 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.