Microarrays

The GPSR maintains technology platforms for two array systems:


Affymetrix GeneChipTM arrays

GeneChip ScannerThe GeneChip system offers multiple array designs to interrogate genome-wide expression profiles of mRNA, lncRNA, and miRNA of human and widely-used model species, as well as many agricultural species.  Information on available expression array options can be found at this link. The GeneChip system operated in the GPSR supports the GeneChip cartridge format which analyzes one labeled sample target per array hybridization. GeneChipPlease note the Affymetrix brand has recently been purchased by ThermoFisher Scientific and is being marketed under their Applied Biosystems product line. For information about GeneChip array solutions for human cytogenetic analysis please click here (Cytogenetic Analysis with Microarrays).  Please contact the core if you are interested in these options. 



GeneChip Scanner
Supports scanning of high density
Affymetrix arrays

Free Affymetrix analysis software - Transcriptome Analysis Console (TAC)

Transcriptome Analysis Software 4.0 - Features include: 

                   - Streamlined QC and data analysis with integration of EC Software and TAC Software into a single tool
                   - Ability to analyze large data sets of 1,000 samples or more
                   - Integration of established LIMMA package
                   - Improved alternative splicing analysis

Please click here to download the TAC software from the ThermoFisher website.  For release notes on TAC 4.0, please click here.


Illumina BeadChip arrays

Illumina BeadChip ArrayThe Illumina HiScan platform supports Infinium high-density (HD) DNA analysis solutions using BeadChip arrays for large-scale interrogations of genome variation.  Infinium assays are available for whole-genome and targeted genotyping and DNA methylation profiling. For methylation analysis, the GPSR is able to provide a complete service from genomic DNA isolation through bisulfite conversion to generation and QC of array data. The BeadChip system is designed with multiple arrays per BeadChip so that sample number minimums are based on BeadChip format and minimum pack sizes. Click here for array options for genotyping and epigenetics analysis.


Illumina HiScan

Supports scanning of high density
Illumina arrays

 

GPSR Array Services

Array assay service fees include a comprehensive quality assessment of the starting material (RNA or DNA), target preparation and QC, array hybridization and initial data quality assessment as well as data archiving. Typical project turnaround time is 2 weeks. To complete a microarray study application, please use the OHSU iLab system.

Sample Preparation and Delivery

For information about sample preparation and delivery, please see the instructions here.