COVID-19 MODIFIED OPERATIONS

OHSU declared modified operations as of March 23rd, 2020, to help slow the spread of the virus that causes COVID-19 (coronavirus disease 2019).  This resulted in the shutdown of all bench activities in the Gene Profiling Shared Resource.

As of June 1,  the GPSR has reopened for research support under OHSU Level 2 modified operations. Laboratory reorganization and PPE and required cleaning procedures have been implement to comply with physical distancing requirements and minimize potential for spreading infection.  Significant changes have been made to sample drop-off procedures and use of shared access instrumentation, so please contact the core before proceeding.   You may continue to request services via iLab.  Please contact Chris Harrington  for questions or more information.  The core team continues to be available to all researchers by email, phone, and online meeting to plan experiments, advise on sample collection and extraction, assist with grant development, review data, and assist with manuscript preparation.

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.

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

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

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.

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 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.

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

  • Postponed: UCSC Genome Browser Workshop
    • This event is postponed as of March 11th, 2020.  This event will be updated once a new workshop date has been determined.
  • 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
  • EPIC methylation arrays for CNS tumor classification
  • Single Cell Analysis
  • Winter 2019 IGL newsletter

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.

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.

Services available for Illumina Infinium genotyping and methylation arrays for low cost whole genome profiling. For more information on this new service, please see Illumina Infinium Microarray Solutions  and array options , or contact Dr. Chris Harringtonfor experimental planning.

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.

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