Microarrays

The GPSR maintains array technology platforms for:

genotyping, cytogenetics, and expression and methylation profiling

Before submitting samples to the core laboratory, please read the instructions or contact one of our staff to discuss requirements. The core team is available to consult on the specifics of sample preparation for your study.

GeneChip scanner: Supports scanning of high density Affymetrix/Applied Biosystems arrays

The 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.  View information on available expression array options. The GeneChip system operated in the GPSR supports the GeneChip cartridge format which analyzes one labeled sample target per array hybridization. Please note the Affymetrix brand has recently been purchased by ThermoFisher Scientific and is being marketed under their Applied Biosystems product line. Visit cytogenetic analysis with microarrays for information about GeneChip array solutions for human cytogenetic analysis.  Please contact the core if you are interested in these options. 

  • Expression Arrays
  • Cytogenetic 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

 Download the TAC software from the ThermoFisher website.  Read release notes on TAC 4.0 for more information.

Illumina HiScan: Supports scanning of high density Illumina arrays

Illumina BeadChip arrays

The 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. View array options for genotyping and epigenetics analysis.  

  • Genotyping Arrays
  • Methylation 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.