Gene Profiling Shared Resource

The Gene Profiling Shared Resource (GPSR) is a unit of the Integrated Genomics Laboratory and is located on OHSU Marquam Hill Campus in Richard Jones Hall, room 5330.  We work closely with the Massively Parallel Sequencing Shared Resource and the DNA Services Core to provide support and services, from specimen processing through data generation and validation.

Please acknowledge support from the core in publications and presentations. 

  • Suggested text: "(Insert appropriate service or platform) were performed in the OHSU Gene Profiling Shared Resource"
    • Services/Platforms: Microarray or qPCR assays, DNA or RNA isolation services, DNA or RNA quality assessments.
  • The Gene Profiling Shared Resource receives support from the OHSU Knight Cancer Institute NCI Cancer Center Support Grant P30CA069533.

Core information flyer 

Services we offer

  • Expression Profiling-Microarrays and qPCR
    • mRNA and microRNA expression profiling, including options for whole transcript analysis and alternative transcript/exon analysis 
  • DNA Variation Analysis-Microarrays and PCR
    • Whole genome and targeted SNP genotyping and copy number analysis with microarrays and PCR assays; methylation profiling with Illumina EPIC arrays
  • RNA and DNA Isolation
    • Support available for RNA/DNA isolation in connection with microarray, sequencing or qPCR projects; automated protocols for QIAGEN spin-column kits, including PAXGene Blood RNA kits
  • RNA Assessment
    • Quantification, size, and/or quality assessment of RNA samples
  • DNA Assessment
    • Quantification, size, and/or quality assessment of DNA samples
  • Consultation
    • For project design and grant development

To request services through the GPSR, go to the iLab website. 

Please see instructions for sample preparation, or contact us, before delivering samples to the core laboratory.

If you would like to request pre-project consultation or request a service that is not represented by one of the categories listed above, please contact Dr. Chris Harrington, GPSR Director.

Major equipment/technologies 

  • Complete Affymetrix GeneChip and Illumina BeadArray systems for array hybridization, processing, and scanning
  • Life Technologies QuantStudio qPCR System for gene expression, genotyping, and more
  • NanoDrop 1000 and 8000 spectrophotometers for nucleic acid quantification
  • SpectraMax i3x Multi-Mode Microplate Reader, a cost-efficient solution for high-sensitivity, high-throughput quantification of RNA and DNA samples
  • Agilent 2100 Bioanalyzer & 2200 TapeStation for RNA and DNA sizing
  • QIAcube & QIAsymphony Sample Prep Robots for automated nucleic acid extractions
  • QIAGEN TissueLyser LT for tissue disruption
  • Eppendorf epMotion 5075 Liquid Handling Robot for sample and reagent aliquoting, and sample normalization and plating
  • Suite of custom and commercial software for data QA/QC and analysis, including Affymetrix Transcriptome Analysis Console

Instrument access we offer

  • QuantStudio 12K Flex real-time PCR System
  • Qiagen QIAcube Sample Prep Robots

Access to these instruments may be scheduled through the GPSR iLab website. 
(Training is required prior to use). If you require more information or assistance using the iLab ordering system, contact Britt Daughtry.

For all other service and instrument access inquiries, please contact the GPSR Director.


For RNA-Seq and DNA-Seq services, please visit the MPSSR website.

For human cell line authentication and oligo synthesis services, please visit the DNA Services Core website.

For study design and analysis support for expression, genotyping and methylation arrays, please contact the OCTRI Translational Bioinformatics Core

Assistance with design, sample preparation, and data analysis for epigenetics projects utilizing RNA-seq, DNA-seq, or Sanger sequencing is available through the KCVI Epigenetics Consortium.


  • Staff Transition
    • Trevor McFarland is leaving the Integrated Genomics Laboratory as of October 1st, 2019. Since 2014, Trevor has applied his knowledge and experience to growing the Gene Profiling Shared Resource and providing excellent support to OHSU researchers.  He will continue to advance scientific research at OHSU in Dr. Julie Saugstad’s laboratory in the Department of Anesthesiology and Preoperative Medicine.
    • Please contact Britt Daughtry or Chris Harrington for information or questions about core services.
  • Summer 2019 IGL newsletter
  • EPIC methylation arrays for CNS tumor classification
  • Choosing between expression arrays and RNA-seq
  • Single Cell Analysis

Assay and technology highlights

  • CytoScan HD arrays for cytogenetics research
    • The CytoScan HD array platform (ThermoFisher Scientific) has 2.7 million markers for copy number analysis. For more information on this cytogenetics research tool, please see information on ThermoFisher's website. Contact Chris Harrington if you are interested in using this platform for your array-based cytogenetics studies.
  • Whole Genome Genotyping and Methylation Analysis with Illumina Array Platform
  • High-throughput DNA/RNA isolation with Qiagen QIAsymphony Isolation Robot
    • Specializing in DNA isolation from human blood and saliva as well as RNA isolation from a variety of specimens including blood and FFPE tissue. Process hundreds of samples a week, reduce isolation turn-around time as well as per sample cost with the added benefit of consistency and reproducibility. For more information, please see the High-Throughput DNA/RNA Isolation flyer, or contact Britt Daughtry.
  • Genome-wide profiling of human, mouse, and rat transcriptome, including Isoforms - ClariomTM arrays
    • Comprehensive transcriptome arrays from Affymetrix (ThermoFisher) : 
    • GeneChip ClariomTM D solutions for human, mouse, and rat. Array design includes exon and splice junction probes and provides data about all transcript isoforms.
    • ClariomTM D solutions for human, mouse, and rat
  • Low cost array option
    • Also available, ClariomTM S solutions for human, mouse, and rat : Gene level whole transcriptome profiling at low cost. Less than $350 per sample for complete service. ClariomTM S solutions for human, mouse, and rat
    • To facilitate analysis of array data, Affymetrix (ThermoFisher) offers easy-to-use Transcriptome Analysis Console (TAC) software for differential expression analysis and data visualization.  For more information about this software that is available at no cost, please contact Kara Sparks at ThermoFisher or Dr. Chris Harrington.

Assays of interest

  • Small sample profiling
    • Improved protocols for small sample profiling – total RNA inputs as low as 100 pg
  • Gene expression and DNA variation assays from biorepository and other fixed specimens
    • Services available for RNA/DNA isolation, qPCR and microarray profiling of FFPE specimens
  • QuantStudio qPCR services