OHSU has lifted COVID 19 modified operations requirements for research laboratories.  The GPSR has returned to normal operations but is retaining enhanced cleaning procedures and some sample pick-up and drop-off modifications and visitor number restrictions.  Please contact Chris Harrington for questions or more information. Core staff are available by email, phone, and online meeting to plan experiments, advise on sample collection and preparation, review data, and assist with grant development and manuscript preparation.  Please submit service requests on our iLab site.

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.  Training and access to many of the core's advanced technology systems is also available.

We focus on DNA and RNA isolation and evaluation, microarrays, real-time PCR and NanoString nCounter assays.

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, qPCR, or NanoString nCounter 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

mRNA and microRNA expression profiling, including options for whole transcript analysis and alternative transcript/exon analysis. 

Whole genome and targeted SNP genotyping and copy number analysis with microarrays and PCR assays; methylation profiling with Illumina EPIC arrays.

Access to NanoString SPRINT Profiler now available.  Complete service option in development.  Please contact Britt Daughtry for information.

Support available for RNA/DNA isolation in connection with microarray, sequencing or qPCR projects; automated protocols for QIAGEN spin-column and magnetic bead-based protocols, including for PAXGene Blood RNA tubes and FFPE samples.

Quantification, size, and/or quality assessment of RNA and DNA samples.

Please contact Chris Harrington for:

  • Project design and grant development
  • Guidance on collection and stabilization of tissue and biofluid samples

Major equipment/technologies 

  • Complete Affymetrix GeneChip system for array hybridization, processing, and scanning
  • Life Technologies QuantStudio qPCR System for gene expression, genotyping, and more
  • NanoString SPRINT Profiler for nCounter® assays
  • 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 & 4200 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 for trained users

  • QuantStudio 12K Flex real-time PCR System
  • Qiagen QIAcube Sample Prep Robots
  • NanoString SPRINT Profiler
  • See DNA Services Core for SpectraMax i3x plate reader

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.

Please contact Britt Daughtry or Chris Harrington for information or questions about core services.

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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.

Announcements/News

Assay and technology highlights

Specializing in DNA isolation from human blood and saliva as well as RNA isolation from a variety of specimens including 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.

Comprehensive transcriptome arrays from Affymetrix (ThermoFisher) : 

Low cost gene expression array option:

  • 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.

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.

Illumina EPIC array analysis support is now available through the Knight Diagnostics Lab.  Please contact Stephen Moore.  If you need support for DNA isolation and QC through the GPSR for downstream array assays, including use of the GeneRead DNA FFPE kit, please contact Britt Daughtry. For assistance with identifying other resources for use of the Infinium array system, please contact 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
  • QuantStudio qPCR services