The OHSU Gene Profiling Shared Resource is transitioning to the Integrated Genomics Laboratory DNA and RNA Services. This unit provides research scientists and clinicians services for RNA expression profiling, DNA variation analysis, and nucleic acid extraction. (Stay tuned, more website updates coming soon).

DNA & RNA Isolations and Gene Profiling Services

DNA and RNA Services is a unit of the Integrated Genomics Laboratory (IGL) and includes all services and technologies formerly provided through the Gene Profiling Shared Resource. We are located on OHSU Marquam Hill Campus in Richard Jones Hall, room 5330. Our unit focuses on DNA and RNA isolation and evaluation, 10X Genomics single-cell cDNA preparation, real-time PCR and NanoString nCounter assays. We work closely with the other units of the IGL 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.

The Integrated Genomics Laboratory DNA and RNA Services unit is now directed by Robert Searles. Please contact the lab manager, Britt Daughtry, if you have any questions.

Please acknowledge support from the core in publications and presentations. 

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

Please submit service requests on our iLab site.

Core information flyer 

Services we offer

Full service support for qPCR mRNA and microRNA expression profiling. Self-service use on both the Quantstudio qPCR systems and the Nanostring SPRINT Profiler.

Multiple single-cell and single-nuclei cDNA preparation options are available on Chromium Controller. This service is coordinated with the Massively Parallel Sequencing Shared Resource (MPSSR) for library preparation and sequencing.  To initiate service, please see the MPSSR's iLab site.

Full service support for targeted SNP genotyping qPCR assays. Self-service use on both the Quantstudio qPCR systems and the Nanostring SPRINT Profiler.

Support available for RNA/DNA isolation for sequencing, qPCR or other gene profiling and DNA analysis applications; automated protocols for QIAGEN spin-column and magnetic bead-based protocols, including for PAXGene Blood RNA tubes and FFPE samples. Services for co-isolation of RNA and DNA as well as Zymo RNA and genomic DNA clean-up services are also available.

RNA and DNA Assessment: Quantification, size, and/or quality assessment of RNA and DNA samples for targeted profiling and genotyping projects.

Please contact Robert Searles for:

  • Grant development and letters of support.

Please contact Britt Daughtry for:

  • Project design, cost estimates, and new service requests.
  • Guidance on collection and stabilization of tissue and biofluid samples.

Major equipment/technologies 

  • Life Technologies QuantStudio qPCR System for gene expression, genotyping, and more
  • NanoString SPRINT Profiler for nCounter® assays
  • NanoDrop One 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

Instrument access for trained users

  • QuantStudio 7 Flex real-time PCR Systems
  • Qiagen QIAcube Sample Prep Robots
  • NanoString SPRINT Profiler
  • 10x Genomics Chromium Controller
  • 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 Robert Searles 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

  • April 25, 2024: OHSU Epigenetics Symposium
    • The OHSU Epigenetics Symposium, organized by the KCVI Epigenetics Consortium, will feature keynote addresses by Dr. Marisa Bartolomei (University of Pennsylvania) and Dr. Joe Ecker (UC San Diego). The program also includes presentations from researchers focused on epigenetics and a poster session featuring graduate students, postdocs, and research staff. A reception will be held at the conclusion of the event.
  • qPCR training seminar
    • The IGL & Thermo Fisher Scientific are hosting a qPCR training seminar (Jan 24th, 2024 from 9am-3pm) that covers basics, applications, software, and instrument operation. Attendees will receive half off an IGL QuantStudio qPCR training - a great opportunity for grad students and new lab members! Register soon as capacity is limited (20 attendees).
  • Winter 2023-2024 Integrated Genomics Laboratory Newsletter
  • Single Cell Analysis
    • The Integrated Genomics Lab cores provide full service support for 10x Genomics RNA-seq, ATAC-seq, and Multiome experiments.
    • Discuss options and best practices for preparing cells and nuclei for 10x Genomics Chromium processing with GPSR staff and 10x Genomics expert.  Click here for more details.
  • NanoString nCounter® technology now available in the core
  • Reciprocal core rate agreement for five Oregon universities
    • Five Oregon universities have signed a new reciprocal internal rate agreement for the use of research core facilities and shared service units for researchers among the institutions

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.

Effective January 1st, 2024, microarray services are no longer offered by the Gene Profiling unit of the Integrated Genomics Laboratory. Several partnering labs offer Affymetrix (ThermoFisher) gene level whole transcriptome profiling at low cost.  For more information about which labs can offer this service please reach out to Chris Harrington.

Illumina EPIC array analysis support is now available through the Knight Diagnostics Lab.  For assistance with identifying other resources for use of the Infinium array system, please contact Chris Harrington.

Assays of interest

  • NanoString nCounter
    • OHSU staff can access the webinar recording for an overview of this technology and core services available.
  • 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

Educational Resources