Illumina Gene Expression Microarrays

Using the Illumina GeneExpression Arrays, the DNA Sequencing Core performs high throughput sample Gene Expression profiling for intact and FFPE RNA samples. The Core Services for the Illumina BeadArray platform consist of the following:

  1. Check RNA quality and quantity– NanoDrop and BioAnalyzer,
  2. Normalize samples
  3. Generate biotin-labeled cRNA,
  4. Perform Illumina GeneExpression Direct Hybridization assay,
  5. Record expression intensities with an iScan Scanner,
  6. Create a GenomeStudio Project for data analysis, and
  7. Generate reports (Internal controls, Samples Table, GroupProbeProfile, SampleProbeProfile).


Illumina Gene Expression Microarrays

Illumina iScan
Primary Contact

Susan Dagenais, Ph.D.
UM DNA Sequencing Core
Phone: 734-615-8743
Fax: 734-763-8889

Typical Cost Click here to view internal pricing list!
Click here to view external pricing list!
Typical Output

For human, >47,000 probes are analyzed to generate a GeneExpression Profile. Illumina offers two GeneExpression Analysis products for mice: 1). >25,000 RefSeq probes analyzed and 2). > 45,000 probes designed from RefSeq, the MEEBO set and the RIKEN FANTOM2 database. For generating Gene Expression Profiles, the iScan is set to record data that can be used with the Illumna GenomeStudio data analysis software package as well as other software such as Bioconductor, GeneSpring, and ArrayExpress.

How to Request

Sample Submission: Contact Susan Dagenais ( and request a Project Quote. Please indicate the number of samples to be assayed and which Illumina BeadChip kit you would like used for the assay. We will e-mail you a Quote for the Illumina Kit costs and estimated Core Processing fees. Once we a signed Quote, we will place an order with Ilumina, assign a Core Project Number, and you will be sent a BeadArray submission form for sample submission.

Sample Requirements

Quantity: We request 100ng/ul (25ul). If you do not have this concentration, please contact Susan Dagenais (

Quality: NanoDrop – the manufacturer of the Illumina TotalPrep RNA Amplification kit recommends that the 260/280 and 260/230 ratios should be >2.0 for best results in generating labled cRNA. A 260/280 ratio <1.8 indicates protein in the prep and a 260/230 ratio <1.5 suggest there is an excess of salts, which may affect amplification.

It is important that the total RNA is free of genomic DNA contamination.

BioAnalyzer – Request that RNAs have a RIN value >8.0 as RNA degradation can lead to incorrect conclusions of the expression data. RNA samples isolated using TRIzol® should be further cleaned by the Qiagen RNA cleanup procedure or the Agencourt RNAClean XP procedure.

RNA QC for quantity and quality is required BEFORE Illumina Whole Genome Gene Expression kit will be ordered.

Typical Turnaround

Typical turnaround time is 2-4 weeks.

Critical Information
  1. The Core will assign Core Sample ID numbers, which you will write on top of 1.5mL tubes containing your samples.
  2. Computer Workstations are available for clients to perform their own analysis using the Illumina GenomeStudio DNA Analysis Software packages.
  3. The Client must perform their own data analysis or consult with a Bio-informatics specialist.
More Information